Electron backscatter diffraction as a domain analysis technique in BiFeO(3)-PbTiO(3) single crystals.

PubMed

Burnett, T L; Comyn, T P; Merson, E; Bell, A J; Mingard, K; Hegarty, T; Cain, M

2008-05-01

xBiFeO(3)-(1-x)PbTiO(3) single crystals were grown via a flux method for a range of compositions. Presented here is a study of the domain configuration in the 0.5BiFeO(3)-0.5PbTiO(3) composition using electron backscatter diffraction to demonstrate the ability of the technique to map ferroelastic domain structures at the micron and submicron scale. The micron-scale domains exhibit an angle of approximately 85 degrees between each variant, indicative of a ferroelastic domain wall in a tetragonal system with a spontaneous strain, c/a - 1 of 0.10, in excellent agreement with the lattice parameters derived from x-ray diffraction. Contrast seen in forescatter images is attributed to variations in the direction of the electrical polarization vector, providing images of ferroelectric domain patterns.

Structural mapping of the coiled-coil domain of a bacterial condensin and comparative analyses across all domains of life suggest conserved features of SMC proteins.

PubMed

Waldman, Vincent M; Stanage, Tyler H; Mims, Alexandra; Norden, Ian S; Oakley, Martha G

2015-06-01

The structural maintenance of chromosomes (SMC) proteins form the cores of multisubunit complexes that are required for the segregation and global organization of chromosomes in all domains of life. These proteins share a common domain structure in which N- and C- terminal regions pack against one another to form a globular ATPase domain. This "head" domain is connected to a central, globular, "hinge" or dimerization domain by a long, antiparallel coiled coil. To date, most efforts for structural characterization of SMC proteins have focused on the globular domains. Recently, however, we developed a method to map interstrand interactions in the 50-nm coiled-coil domain of MukB, the divergent SMC protein found in γ-proteobacteria. Here, we apply that technique to map the structure of the Bacillus subtilis SMC (BsSMC) coiled-coil domain. We find that, in contrast to the relatively complicated coiled-coil domain of MukB, the BsSMC domain is nearly continuous, with only two detectable coiled-coil interruptions. Near the middle of the domain is a break in coiled-coil structure in which there are three more residues on the C-terminal strand than on the N-terminal strand. Close to the head domain, there is a second break with a significantly longer insertion on the same strand. These results provide an experience base that allows an informed interpretation of the output of coiled-coil prediction algorithms for this family of proteins. A comparison of such predictions suggests that these coiled-coil deviations are highly conserved across SMC types in a wide variety of organisms, including humans. © 2015 Wiley Periodicals, Inc.

A vector scanning processing technique for pulsed laser velocimetry

NASA Technical Reports Server (NTRS)

Wernet, Mark P.; Edwards, Robert V.

1989-01-01

Pulsed laser sheet velocimetry yields nonintrusive measurements of two-dimensional velocity vectors across an extended planar region of a flow. Current processing techniques offer high precision (1 pct) velocity estimates, but can require several hours of processing time on specialized array processors. Under some circumstances, a simple, fast, less accurate (approx. 5 pct), data reduction technique which also gives unambiguous velocity vector information is acceptable. A direct space domain processing technique was examined. The direct space domain processing technique was found to be far superior to any other techniques known, in achieving the objectives listed above. It employs a new data coding and reduction technique, where the particle time history information is used directly. Further, it has no 180 deg directional ambiguity. A complex convection vortex flow was recorded and completely processed in under 2 minutes on an 80386 based PC, producing a 2-D velocity vector map of the flow field. Hence, using this new space domain vector scanning (VS) technique, pulsed laser velocimetry data can be reduced quickly and reasonably accurately, without specialized array processing hardware.

Advanced Ecosystem Mapping Techniques for Large Arctic Study Domains Using Calibrated High-Resolution Imagery

NASA Astrophysics Data System (ADS)

Macander, M. J.; Frost, G. V., Jr.

2015-12-01

Regional-scale mapping of vegetation and other ecosystem properties has traditionally relied on medium-resolution remote sensing such as Landsat (30 m) and MODIS (250 m). Yet, the burgeoning availability of high-resolution (<=2 m) imagery and ongoing advances in computing power and analysis tools raises the prospect of performing ecosystem mapping at fine spatial scales over large study domains. Here we demonstrate cutting-edge mapping approaches over a ~35,000 km² study area on Alaska's North Slope using calibrated and atmospherically-corrected mosaics of high-resolution WorldView-2 and GeoEye-1 imagery: (1) an a priori spectral approach incorporating the Satellite Imagery Automatic Mapper (SIAM) algorithms; (2) image segmentation techniques; and (3) texture metrics. The SIAM spectral approach classifies radiometrically-calibrated imagery to general vegetation density categories and non-vegetated classes. The SIAM classes were developed globally and their applicability in arctic tundra environments has not been previously evaluated. Image segmentation, or object-based image analysis, automatically partitions high-resolution imagery into homogeneous image regions that can then be analyzed based on spectral, textural, and contextual information. We applied eCognition software to delineate waterbodies and vegetation classes, in combination with other techniques. Texture metrics were evaluated to determine the feasibility of using high-resolution imagery to algorithmically characterize periglacial surface forms (e.g., ice-wedge polygons), which are an important physical characteristic of permafrost-dominated regions but which cannot be distinguished by medium-resolution remote sensing. These advanced mapping techniques provide products which can provide essential information supporting a broad range of ecosystem science and land-use planning applications in northern Alaska and elsewhere in the circumpolar Arctic.

[Visualizing Research Lines in Public Health: An analysis Based on Bibliometric Maps Applied to the Revista Española de Salud Pública (2006-2015)].

PubMed

Gálvez, Carmen

2016-12-01

Identifying research lines is essential to understand the knowledge structure of a scientific domain. The aim of this study was to identify the main research topics of within the domain of public health, in the Revista Española de Saslud Pública during 2006-2015. Original articles included in the Social Sciences Citation Index (SSCI) database, available online through the Web of Science (WoS), were selected. The analysis units used were the keywords, KeyWords Plus (KW+), extracted automatically by SSCI. With KW+ obtained bibliometric, maps were created using a methodology based on the combination of co-word analysis, co-word analysis, clustering techniques and visualization techniques. We analyzed 512 documents, of which 176 KW+ were obtained with a frequency greater than or equal to 3. The results were bidimensional bibliometric maps with thematic groupings of KW+, representing the main research fronts: i) epidemiology, risk control programs disease and, in general, service organization and health policies; ii) infectious diseases, principally HIV; iii) a progressive increase in several lines interrelated with cardiovascular diseases (CVD); iv) a line multidimensional dedicated to different aspects associated to the quality of life related to health (HRQoL); and v) an emerging line linked to binge drinking. For the multidisciplinary and multidimensional nature of public health, the construction of bibliometric maps is an appropriate methodology to understand the knowledge structure of this scientific domain.

Recent developments in machine learning applications in landslide susceptibility mapping

NASA Astrophysics Data System (ADS)

Lun, Na Kai; Liew, Mohd Shahir; Matori, Abdul Nasir; Zawawi, Noor Amila Wan Abdullah

2017-11-01

While the prediction of spatial distribution of potential landslide occurrences is a primary interest in landslide hazard mitigation, it remains a challenging task. To overcome the scarceness of complete, sufficiently detailed geomorphological attributes and environmental conditions, various machine-learning techniques are increasingly applied to effectively map landslide susceptibility for large regions. Nevertheless, limited review papers are devoted to this field, particularly on the various domain specific applications of machine learning techniques. Available literature often report relatively good predictive performance, however, papers discussing the limitations of each approaches are quite uncommon. The foremost aim of this paper is to narrow these gaps in literature and to review up-to-date machine learning and ensemble learning techniques applied in landslide susceptibility mapping. It provides new readers an introductory understanding on the subject matter and researchers a contemporary review of machine learning advancements alongside the future direction of these techniques in the landslide mitigation field.

Simplified Parallel Domain Traversal

DOE Office of Scientific and Technical Information (OSTI.GOV)

Erickson III, David J

2011-01-01

Many data-intensive scientific analysis techniques require global domain traversal, which over the years has been a bottleneck for efficient parallelization across distributed-memory architectures. Inspired by MapReduce and other simplified parallel programming approaches, we have designed DStep, a flexible system that greatly simplifies efficient parallelization of domain traversal techniques at scale. In order to deliver both simplicity to users as well as scalability on HPC platforms, we introduce a novel two-tiered communication architecture for managing and exploiting asynchronous communication loads. We also integrate our design with advanced parallel I/O techniques that operate directly on native simulation output. We demonstrate DStep bymore » performing teleconnection analysis across ensemble runs of terascale atmospheric CO{sub 2} and climate data, and we show scalability results on up to 65,536 IBM BlueGene/P cores.« less

In vitro and in vivo mapping of the Prunus necrotic ringspot virus coat protein C-terminal dimerization domain by bimolecular fluorescence complementation.

PubMed

Aparicio, Frederic; Sánchez-Navarro, Jesús A; Pallás, Vicente

2006-06-01

Interactions between viral proteins are critical for virus viability. Bimolecular fluorescent complementation (BiFC) technique determines protein interactions in real-time under almost normal physiological conditions. The coat protein (CP) of Prunus necrotic ringspot virus is required for multiple functions in its replication cycle. In this study, the region involved in CP dimerization has been mapped by BiFC in both bacteria and plant tissue. Full-length and C-terminal deleted forms of the CP gene were fused in-frame to the N- and C-terminal fragments of the yellow fluorescent protein. The BiFC analysis showed that a domain located between residues 9 and 27 from the C-end plays a critical role in dimerization. The importance of this C-terminal region in dimer formation and the applicability of the BiFC technique to analyse viral protein interactions are discussed.

Mapping to Irregular Torus Topologies and Other Techniques for Petascale Biomolecular Simulation

PubMed Central

Phillips, James C.; Sun, Yanhua; Jain, Nikhil; Bohm, Eric J.; Kalé, Laxmikant V.

2014-01-01

Currently deployed petascale supercomputers typically use toroidal network topologies in three or more dimensions. While these networks perform well for topology-agnostic codes on a few thousand nodes, leadership machines with 20,000 nodes require topology awareness to avoid network contention for communication-intensive codes. Topology adaptation is complicated by irregular node allocation shapes and holes due to dedicated input/output nodes or hardware failure. In the context of the popular molecular dynamics program NAMD, we present methods for mapping a periodic 3-D grid of fixed-size spatial decomposition domains to 3-D Cray Gemini and 5-D IBM Blue Gene/Q toroidal networks to enable hundred-million atom full machine simulations, and to similarly partition node allocations into compact domains for smaller simulations using multiple-copy algorithms. Additional enabling techniques are discussed and performance is reported for NCSA Blue Waters, ORNL Titan, ANL Mira, TACC Stampede, and NERSC Edison. PMID:25594075

Spatial frequency domain spectroscopy of two layer media

NASA Astrophysics Data System (ADS)

Yudovsky, Dmitry; Durkin, Anthony J.

2011-10-01

Monitoring of tissue blood volume and oxygen saturation using biomedical optics techniques has the potential to inform the assessment of tissue health, healing, and dysfunction. These quantities are typically estimated from the contribution of oxyhemoglobin and deoxyhemoglobin to the absorption spectrum of the dermis. However, estimation of blood related absorption in superficial tissue such as the skin can be confounded by the strong absorption of melanin in the epidermis. Furthermore, epidermal thickness and pigmentation varies with anatomic location, race, gender, and degree of disease progression. This study describes a technique for decoupling the effect of melanin absorption in the epidermis from blood absorption in the dermis for a large range of skin types and thicknesses. An artificial neural network was used to map input optical properties to spatial frequency domain diffuse reflectance of two layer media. Then, iterative fitting was used to determine the optical properties from simulated spatial frequency domain diffuse reflectance. Additionally, an artificial neural network was trained to directly map spatial frequency domain reflectance to sets of optical properties of a two layer medium, thus bypassing the need for iteration. In both cases, the optical thickness of the epidermis and absorption and reduced scattering coefficients of the dermis were determined independently. The accuracy and efficiency of the iterative fitting approach was compared with the direct neural network inversion.

An efficient depth map preprocessing method based on structure-aided domain transform smoothing for 3D view generation

PubMed Central

Ma, Liyan; Qiu, Bo; Cui, Mingyue; Ding, Jianwei

2017-01-01

Depth image-based rendering (DIBR), which is used to render virtual views with a color image and the corresponding depth map, is one of the key techniques in the 2D to 3D conversion process. Due to the absence of knowledge about the 3D structure of a scene and its corresponding texture, DIBR in the 2D to 3D conversion process, inevitably leads to holes in the resulting 3D image as a result of newly-exposed areas. In this paper, we proposed a structure-aided depth map preprocessing framework in the transformed domain, which is inspired by recently proposed domain transform for its low complexity and high efficiency. Firstly, our framework integrates hybrid constraints including scene structure, edge consistency and visual saliency information in the transformed domain to improve the performance of depth map preprocess in an implicit way. Then, adaptive smooth localization is cooperated and realized in the proposed framework to further reduce over-smoothness and enhance optimization in the non-hole regions. Different from the other similar methods, the proposed method can simultaneously achieve the effects of hole filling, edge correction and local smoothing for typical depth maps in a united framework. Thanks to these advantages, it can yield visually satisfactory results with less computational complexity for high quality 2D to 3D conversion. Numerical experimental results demonstrate the excellent performances of the proposed method. PMID:28407027

Design of Digital Phase-Locked Loops For Advanced Digital Transponders

NASA Technical Reports Server (NTRS)

Nguyen, Tien M.

1994-01-01

For advanced digital space transponders, the Digital Phased-Locked Loops (DPLLs) can be designed using the available analog loops. DPLLs considered in this paper are derived from the Analog Phase-Locked Loop (APLL) using S-domain mapping techniques.

Color image cryptosystem using Fresnel diffraction and phase modulation in an expanded fractional Fourier transform domain

NASA Astrophysics Data System (ADS)

Chen, Hang; Liu, Zhengjun; Chen, Qi; Blondel, Walter; Varis, Pierre

2018-05-01

In this letter, what we believe is a new technique for optical color image encryption by using Fresnel diffraction and a phase modulation in an extended fractional Fourier transform domain is proposed. Different from the RGB component separation based method, the color image is converted into one component by improved Chirikov mapping. The encryption system is addressed with Fresnel diffraction and phase modulation. A pair of lenses is placed into the fractional Fourier transform system for the modulation of beam propagation. The structure parameters of the optical system and parameters in Chirikov mapping serve as extra keys. Some numerical simulations are given to test the validity of the proposed cryptosystem.

Characterization of a subwavelength-scale 3D void structure using the FDTD-based confocal laser scanning microscopic image mapping technique.

PubMed

Choi, Kyongsik; Chon, James W; Gu, Min; Lee, Byoungho

2007-08-20

In this paper, a simple confocal laser scanning microscopic (CLSM) image mapping technique based on the finite-difference time domain (FDTD) calculation has been proposed and evaluated for characterization of a subwavelength-scale three-dimensional (3D) void structure fabricated inside polymer matrix. The FDTD simulation method adopts a focused Gaussian beam incident wave, Berenger's perfectly matched layer absorbing boundary condition, and the angular spectrum analysis method. Through the well matched simulation and experimental results of the xz-scanned 3D void structure, we first characterize the exact position and the topological shape factor of the subwavelength-scale void structure, which was fabricated by a tightly focused ultrashort pulse laser. The proposed CLSM image mapping technique based on the FDTD can be widely applied from the 3D near-field microscopic imaging, optical trapping, and evanescent wave phenomenon to the state-of-the-art bio- and nanophotonics.

An analysis of scatter decomposition

NASA Technical Reports Server (NTRS)

Nicol, David M.; Saltz, Joel H.

1990-01-01

A formal analysis of a powerful mapping technique known as scatter decomposition is presented. Scatter decomposition divides an irregular computational domain into a large number of equal sized pieces, and distributes them modularly among processors. A probabilistic model of workload in one dimension is used to formally explain why, and when scatter decomposition works. The first result is that if correlation in workload is a convex function of distance, then scattering a more finely decomposed domain yields a lower average processor workload variance. The second result shows that if the workload process is stationary Gaussian and the correlation function decreases linearly in distance until becoming zero and then remains zero, scattering a more finely decomposed domain yields a lower expected maximum processor workload. Finally it is shown that if the correlation function decreases linearly across the entire domain, then among all mappings that assign an equal number of domain pieces to each processor, scatter decomposition minimizes the average processor workload variance. The dependence of these results on the assumption of decreasing correlation is illustrated with situations where a coarser granularity actually achieves better load balance.

The burden of neck pain: its meaning for persons with neck pain and healthcare providers, explored by concept mapping.

PubMed

van Randeraad-van der Zee, Carlijn H; Beurskens, Anna J H M; Swinkels, Raymond A H M; Pool, Jan J M; Batterham, Roy W; Osborne, Richard H; de Vet, Henrica C W

2016-05-01

To empirically define the concept of burden of neck pain. The lack of a clear understanding of this construct from the perspective of persons with neck pain and care providers hampers adequate measurement of this burden. An additional aim was to compare the conceptual model obtained with the frequently used Neck Disability Index (NDI). Concept mapping, combining qualitative (nominal group technique and group consensus) and quantitative research methods (cluster analysis and multidimensional scaling), was applied to groups of persons with neck pain (n = 3) and professionals treating persons with neck pain (n = 2). Group members generated statements, which were organized into concept maps. Group members achieved consensus about the number and description of domains and the researchers then generated an overall mind map covering the full breadth of the burden of neck pain. Concept mapping revealed 12 domains of burden of neck pain: impaired mobility neck, neck pain, fatigue/concentration, physical complaints, psychological aspects/consequences, activities of daily living, social participation, financial consequences, difficult to treat/difficult to diagnose, difference of opinion with care providers, incomprehension by social environment, and how person with neck pain deal with complaints. All ten items of the NDI could be linked to the mind map, but the NDI measures only part of the burden of neck pain. This study revealed the relevant domains for the burden of neck pain from the viewpoints of persons with neck pain and their care providers. These results can guide the identification of existing measurements instruments for each domain or the development of new ones to measure the burden of neck pain.

An image morphing technique based on optimal mass preserving mapping.

PubMed

Zhu, Lei; Yang, Yan; Haker, Steven; Tannenbaum, Allen

2007-06-01

Image morphing, or image interpolation in the time domain, deals with the metamorphosis of one image into another. In this paper, a new class of image morphing algorithms is proposed based on the theory of optimal mass transport. The L(2) mass moving energy functional is modified by adding an intensity penalizing term, in order to reduce the undesired double exposure effect. It is an intensity-based approach and, thus, is parameter free. The optimal warping function is computed using an iterative gradient descent approach. This proposed morphing method is also extended to doubly connected domains using a harmonic parameterization technique, along with finite-element methods.

An Image Morphing Technique Based on Optimal Mass Preserving Mapping

PubMed Central

Zhu, Lei; Yang, Yan; Haker, Steven; Tannenbaum, Allen

2013-01-01

Image morphing, or image interpolation in the time domain, deals with the metamorphosis of one image into another. In this paper, a new class of image morphing algorithms is proposed based on the theory of optimal mass transport. The L2 mass moving energy functional is modified by adding an intensity penalizing term, in order to reduce the undesired double exposure effect. It is an intensity-based approach and, thus, is parameter free. The optimal warping function is computed using an iterative gradient descent approach. This proposed morphing method is also extended to doubly connected domains using a harmonic parameterization technique, along with finite-element methods. PMID:17547128

Deep data analysis via physically constrained linear unmixing: universal framework, domain examples, and a community-wide platform.

PubMed

Kannan, R; Ievlev, A V; Laanait, N; Ziatdinov, M A; Vasudevan, R K; Jesse, S; Kalinin, S V

2018-01-01

Many spectral responses in materials science, physics, and chemistry experiments can be characterized as resulting from the superposition of a number of more basic individual spectra. In this context, unmixing is defined as the problem of determining the individual spectra, given measurements of multiple spectra that are spatially resolved across samples, as well as the determination of the corresponding abundance maps indicating the local weighting of each individual spectrum. Matrix factorization is a popular linear unmixing technique that considers that the mixture model between the individual spectra and the spatial maps is linear. Here, we present a tutorial paper targeted at domain scientists to introduce linear unmixing techniques, to facilitate greater understanding of spectroscopic imaging data. We detail a matrix factorization framework that can incorporate different domain information through various parameters of the matrix factorization method. We demonstrate many domain-specific examples to explain the expressivity of the matrix factorization framework and show how the appropriate use of domain-specific constraints such as non-negativity and sum-to-one abundance result in physically meaningful spectral decompositions that are more readily interpretable. Our aim is not only to explain the off-the-shelf available tools, but to add additional constraints when ready-made algorithms are unavailable for the task. All examples use the scalable open source implementation from https://github.com/ramkikannan/nmflibrary that can run from small laptops to supercomputers, creating a user-wide platform for rapid dissemination and adoption across scientific disciplines.

Deriving Lifetime Maps in the Time/Frequency Domain of Coherent Structures in the Turbulent Boundary Layer

NASA Technical Reports Server (NTRS)

Palumbo, Dan

2008-01-01

The lifetimes of coherent structures are derived from data correlated over a 3 sensor array sampling streamwise sidewall pressure at high Reynolds number (> 10(exp 8)). The data were acquired at subsonic, transonic and supersonic speeds aboard a Tupolev Tu-144. The lifetimes are computed from a variant of the correlation length termed the lifelength. Characteristic lifelengths are estimated by fitting a Gaussian distribution to the sensors cross spectra and are shown to compare favorably with Efimtsov s prediction of correlation space scales. Lifelength distributions are computed in the time/frequency domain using an interval correlation technique on the continuous wavelet transform of the original time data. The median values of the lifelength distributions are found to be very close to the frequency averaged result. The interval correlation technique is shown to allow the retrieval and inspection of the original time data of each event in the lifelength distributions, thus providing a means to locate and study the nature of the coherent structure in the turbulent boundary layer. The lifelength data are converted to lifetimes using the convection velocity. The lifetime of events in the time/frequency domain are displayed in Lifetime Maps. The primary purpose of the paper is to validate these new analysis techniques so that they can be used with confidence to further characterize the behavior of coherent structures in the turbulent boundary layer.

Site-directed DNA crosslinking of large multisubunit protein-DNA complexes.

PubMed

Persinger, Jim; Bartholomew, Blaine

2009-01-01

Several methods have been developed to site-specifically incorporate photoreactive nucleotide analogs into DNA for the purpose of identifying the proteins and their domains that are in contact with particular regions of DNA. The synthesis of several deoxynucleotide analogs that have a photoreactive group tethered to the nucleotide base and the incorporation of these analogs into DNA are described. In a second approach, oligonucleotide with a photoreactive group attached to the phosphate backbone is chemically synthesized. The photoreactive oligonucleotide is then enzymatically incorporated into DNA by annealing it to a complementary DNA template and extending with DNA polymerase. Both approaches have been effectively used to map protein-DNA interactions in large multisubunit complexes such as the eukaryotic transcription or ATP-dependent chromatin remodeling complexes. Not only do these techniques map the binding sites of the various subunits in these complexes, but when coupled with peptide mapping also determine the protein domain that is in close proximity to the different DNA sites. The strength of these techniques is the ability to scan a large number of potential sites by making combinations of different DNA probes and is facilitated by using an immobilized DNA template for synthesis.

Visualizing the Topical Structure of the Medical Sciences: A Self-Organizing Map Approach

PubMed Central

Skupin, André; Biberstine, Joseph R.; Börner, Katy

2013-01-01

Background We implement a high-resolution visualization of the medical knowledge domain using the self-organizing map (SOM) method, based on a corpus of over two million publications. While self-organizing maps have been used for document visualization for some time, (1) little is known about how to deal with truly large document collections in conjunction with a large number of SOM neurons, (2) post-training geometric and semiotic transformations of the SOM tend to be limited, and (3) no user studies have been conducted with domain experts to validate the utility and readability of the resulting visualizations. Our study makes key contributions to all of these issues. Methodology Documents extracted from Medline and Scopus are analyzed on the basis of indexer-assigned MeSH terms. Initial dimensionality is reduced to include only the top 10% most frequent terms and the resulting document vectors are then used to train a large SOM consisting of over 75,000 neurons. The resulting two-dimensional model of the high-dimensional input space is then transformed into a large-format map by using geographic information system (GIS) techniques and cartographic design principles. This map is then annotated and evaluated by ten experts stemming from the biomedical and other domains. Conclusions Study results demonstrate that it is possible to transform a very large document corpus into a map that is visually engaging and conceptually stimulating to subject experts from both inside and outside of the particular knowledge domain. The challenges of dealing with a truly large corpus come to the fore and require embracing parallelization and use of supercomputing resources to solve otherwise intractable computational tasks. Among the envisaged future efforts are the creation of a highly interactive interface and the elaboration of the notion of this map of medicine acting as a base map, onto which other knowledge artifacts could be overlaid. PMID:23554924

Analysis of neoplastic lesions in magnetic resonance imaging using self-organizing maps.

PubMed

Mei, Paulo Afonso; de Carvalho Carneiro, Cleyton; Fraser, Stephen J; Min, Li Li; Reis, Fabiano

2015-12-15

To provide an improved method for the identification and analysis of brain tumors in MRI scans using a semi-automated computational approach, that has the potential to provide a more objective, precise and quantitatively rigorous analysis, compared to human visual analysis. Self-Organizing Maps (SOM) is an unsupervised, exploratory data analysis tool, which can automatically domain an image into selfsimilar regions or clusters, based on measures of similarity. It can be used to perform image-domain of brain tissue on MR images, without prior knowledge. We used SOM to analyze T1, T2 and FLAIR acquisitions from two MRI machines in our service from 14 patients with brain tumors confirmed by biopsies--three lymphomas, six glioblastomas, one meningioma, one ganglioglioma, two oligoastrocytomas and one astrocytoma. The SOM software was used to analyze the data from the three image acquisitions from each patient and generated a self-organized map for each containing 25 clusters. Damaged tissue was separated from the normal tissue using the SOM technique. Furthermore, in some cases it allowed to separate different areas from within the tumor--like edema/peritumoral infiltration and necrosis. In lesions with less precise boundaries in FLAIR, the estimated damaged tissue area in the resulting map appears bigger. Our results showed that SOM has the potential to be a powerful MR imaging analysis technique for the assessment of brain tumors. Copyright © 2015. Published by Elsevier B.V.

The DIMA web resource--exploring the protein domain network.

PubMed

Pagel, Philipp; Oesterheld, Matthias; Stümpflen, Volker; Frishman, Dmitrij

2006-04-15

Conserved domains represent essential building blocks of most known proteins. Owing to their role as modular components carrying out specific functions they form a network based both on functional relations and direct physical interactions. We have previously shown that domain interaction networks provide substantially novel information with respect to networks built on full-length protein chains. In this work we present a comprehensive web resource for exploring the Domain Interaction MAp (DIMA), interactively. The tool aims at integration of multiple data sources and prediction techniques, two of which have been implemented so far: domain phylogenetic profiling and experimentally demonstrated domain contacts from known three-dimensional structures. A powerful yet simple user interface enables the user to compute, visualize, navigate and download domain networks based on specific search criteria. http://mips.gsf.de/genre/proj/dima

Comprehensive analysis of TEM methods for LiFePO4/FePO4 phase mapping: spectroscopic techniques (EFTEM, STEM-EELS) and STEM diffraction techniques (ACOM-TEM).

PubMed

Mu, X; Kobler, A; Wang, D; Chakravadhanula, V S K; Schlabach, S; Szabó, D V; Norby, P; Kübel, C

2016-11-01

Transmission electron microscopy (TEM) has been used intensively in investigating battery materials, e.g. to obtain phase maps of partially (dis)charged (lithium) iron phosphate (LFP/FP), which is one of the most promising cathode material for next generation lithium ion (Li-ion) batteries. Due to the weak interaction between Li atoms and fast electrons, mapping of the Li distribution is not straightforward. In this work, we revisited the issue of TEM measurements of Li distribution maps for LFP/FP. Different TEM techniques, including spectroscopic techniques (energy filtered (EF)TEM in the energy range from low-loss to core-loss) and a STEM diffraction technique (automated crystal orientation mapping (ACOM)), were applied to map the lithiation of the same location in the same sample. This enabled a direct comparison of the results. The maps obtained by all methods showed excellent agreement with each other. Because of the strong difference in the imaging mechanisms, it proves the reliability of both the spectroscopic and STEM diffraction phase mapping. A comprehensive comparison of all methods is given in terms of information content, dose level, acquisition time and signal quality. The latter three are crucial for the design of in-situ experiments with beam sensitive Li-ion battery materials. Furthermore, we demonstrated the power of STEM diffraction (ACOM-STEM) providing additional crystallographic information, which can be analyzed to gain a deeper understanding of the LFP/FP interface properties such as statistical information on phase boundary orientation and misorientation between domains. Copyright © 2016 Elsevier B.V. All rights reserved.

Topographic gravity modeling for global Bouguer maps to degree 2160: Validation of spectral and spatial domain forward modeling techniques at the 10 microGal level

NASA Astrophysics Data System (ADS)

Hirt, Christian; Reußner, Elisabeth; Rexer, Moritz; Kuhn, Michael

2016-09-01

Over the past years, spectral techniques have become a standard to model Earth's global gravity field to 10 km scales, with the EGM2008 geopotential model being a prominent example. For some geophysical applications of EGM2008, particularly Bouguer gravity computation with spectral techniques, a topographic potential model of adequate resolution is required. However, current topographic potential models have not yet been successfully validated to degree 2160, and notable discrepancies between spectral modeling and Newtonian (numerical) integration well beyond the 10 mGal level have been reported. Here we accurately compute and validate gravity implied by a degree 2160 model of Earth's topographic masses. Our experiments are based on two key strategies, both of which require advanced computational resources. First, we construct a spectrally complete model of the gravity field which is generated by the degree 2160 Earth topography model. This involves expansion of the topographic potential to the 15th integer power of the topography and modeling of short-scale gravity signals to ultrahigh degree of 21,600, translating into unprecedented fine scales of 1 km. Second, we apply Newtonian integration in the space domain with high spatial resolution to reduce discretization errors. Our numerical study demonstrates excellent agreement (8 μGgal RMS) between gravity from both forward modeling techniques and provides insight into the convergence process associated with spectral modeling of gravity signals at very short scales (few km). As key conclusion, our work successfully validates the spectral domain forward modeling technique for degree 2160 topography and increases the confidence in new high-resolution global Bouguer gravity maps.

Age mapping and dating of monazite on the electron microprobe: Deconvoluting multistage tectonic histories

NASA Astrophysics Data System (ADS)

Williams, Michael L.; Jercinovic, Michael J.; Terry, Michael P.

1999-11-01

High-resolution X-ray mapping and dating of monazite on the electron microprobe are powerful geochronological tools for structural, metamorphic, and tectonic analysis. X-ray maps commonly show complex Th, U, and Pb zoning that reflects monazite growth and overgrowth events. Age maps constructed from the X-ray maps simplify the zoning and highlight age domains. Microprobe dating offers a rapid, in situ method for estimating ages of mapped domains. Application of these techniques has placed new constraints on the tectonic history of three areas. In western Canada, age mapping has revealed multiphase monazite, with older cores and younger rims, included in syntectonic garnet. Microprobe ages show that tectonism occurred ca. 1.9 Ga, 700 m.y. later than mylonitization in the adjacent Snowbird tectonic zone. In New Mexico, age mapping and dating show that the dominant fabric and triple-point metamorphism occurred during a 1.4 Ga reactivation, not during the 1.7 Ga Yavapai-Mazatzal orogeny. In Norway, monazite inclusions in garnet constrain high-pressure metamorphism to ca. 405 Ma, and older cores indicate a previously unrecognized component of ca. 1.0 Ga monazite. In all three areas, microprobe dating and age mapping have provided a critical textural context for geochronologic data and a better understanding of the complex age spectra of these multistage orogenic belts.

Modulated scattering technique in the terahertz domain enabled by current actuated vanadium dioxide switches

PubMed Central

Vitale, W. A.; Tamagnone, M.; Émond, N.; Le Drogoff, B.; Capdevila, S.; Skrivervik, A.; Chaker, M.; Mosig, J. R.; Ionescu, A. M.

2017-01-01

The modulated scattering technique is based on the use of reconfigurable electromagnetic scatterers, structures able to scatter and modulate an impinging electromagnetic field in function of a control signal. The modulated scattering technique is used in a wide range of frequencies up to millimeter waves for various applications, such as field mapping of circuits or antennas, radio-frequency identification devices and imaging applications. However, its implementation in the terahertz domain remains challenging. Here, we describe the design and experimental demonstration of the modulated scattering technique at terahertz frequencies. We characterize a modulated scatterer consisting in a bowtie antenna loaded with a vanadium dioxide switch, actuated using a continuous current. The modulated scatterer behavior is demonstrated using a time domain terahertz spectroscopy setup and shows significant signal strength well above 0.5 THz, which makes this device a promising candidate for the development of fast and energy-efficient THz communication devices and imaging systems. Moreover, our experiments allowed us to verify the operation of a single micro-meter sized VO2 switch at terahertz frequencies, thanks to the coupling provided by the antenna. PMID:28145523

New Inversion and Interpretation of Public-Domain Electromagnetic Survey Data from Selected Areas in Alaska

NASA Astrophysics Data System (ADS)

Smith, B. D.; Kass, A.; Saltus, R. W.; Minsley, B. J.; Deszcz-Pan, M.; Bloss, B. R.; Burns, L. E.

2013-12-01

Public-domain airborne geophysical surveys (combined electromagnetics and magnetics), mostly collected for and released by the State of Alaska, Division of Geological and Geophysical Surveys (DGGS), are a unique and valuable resource for both geologic interpretation and geophysical methods development. A new joint effort by the US Geological Survey (USGS) and the DGGS aims to add value to these data through the application of novel advanced inversion methods and through innovative and intuitive display of data: maps, profiles, voxel-based models, and displays of estimated inversion quality and confidence. Our goal is to make these data even more valuable for interpretation of geologic frameworks, geotechnical studies, and cryosphere studies, by producing robust estimates of subsurface resistivity that can be used by non-geophysicists. The available datasets, which are available in the public domain, include 39 frequency-domain electromagnetic datasets collected since 1993, and continue to grow with 5 more data releases pending in 2013. The majority of these datasets were flown for mineral resource purposes, with one survey designed for infrastructure analysis. In addition, several USGS datasets are included in this study. The USGS has recently developed new inversion methodologies for airborne EM data and have begun to apply these and other new techniques to the available datasets. These include a trans-dimensional Markov Chain Monte Carlo technique, laterally-constrained regularized inversions, and deterministic inversions which include calibration factors as a free parameter. Incorporation of the magnetic data as an additional constraining dataset has also improved the inversion results. Processing has been completed in several areas, including Fortymile and the Alaska Highway surveys, and continues in others such as the Styx River and Nome surveys. Utilizing these new techniques, we provide models beyond the apparent resistivity maps supplied by the original contractors, allowing us to produce a variety of products, such as maps of resistivity as a function of depth or elevation, cross section maps, and 3D voxel models, which have been treated consistently both in terms of processing and error analysis throughout the state. These products facilitate a more fruitful exchange between geologists and geophysicists and a better understanding of uncertainty, and the process results in iterative development and improvement of geologic models, both on small and large scales.

Systematic Representation of Knowledge of Ecology: Concepts and Relationships.

ERIC Educational Resources Information Center

Garb, Yaakov; And Others

This study describes efforts to apply principles of systematic knowledge representation (concept mapping and computer-based semantic networking techniques) to the domain of ecology. A set of 24 relationships and modifiers is presented that seem sufficient for describing all ecological relationships discussed in an introductory course. Many of…

Localization of Stable and Chaotic Nonpropagating Structures in Nonlinear Mesoscopic Lattices.

NASA Astrophysics Data System (ADS)

Greenfield, Alan Barry

Recent developments in the study of non-linear localized states, especially non-propagating ones, are outlined. Theoretical models of linear and nonlinear states in a lattice of coupled pendulums and related systems are reviewed. Particular attention is paid to those states which can be described by the Nonlinear Schrodinger equation as well as states where two modes can coexist and states exhibiting chaos. Measurement of localized stable and chaotic states in a 35 site physical pendulum lattice is reported. Various measurement techniques that were used are explained. States that were measured include the tanh profile or kink soliton, and the corresponding uniform state in the wavelength 2 mode, a similar soliton and uniform state in the wavelength 4 mode, a domain wall between the wavelength 2 and 4 modes and a domain wall between a chaotic state and the wavelength 2 mode. Amplitude profiles were measured for the stable kink and domain wall states and smooth curves were obtained by dividing the kink states by the corresponding uniform states. Return maps were measured for two sites in the chaotic domain wall. Simulation of a chaotic domain wall in a 50 site numerical lattice is reported. This system has the advantage that its parameters can be modified much more easily than those of the physical lattice. An attempt is made at quantifying the level of chaos as a function of lattice site with fractal dimension calculations on return maps embedded in a three dimensional space. The drive plane of the chaotic domain wall is mapped out in the drive amplitude - drive frequency plane. Transitions to various stable and quasiperiodic domain walls are noted.

A main path domain map as digital library interface

NASA Astrophysics Data System (ADS)

Demaine, Jeffrey

2009-01-01

The shift to electronic publishing of scientific journals is an opportunity for the digital library to provide non-traditional ways of accessing the literature. One method is to use citation metadata drawn from a collection of electronic journals to generate maps of science. These maps visualize the communication patterns in the collection, giving the user an easy-tograsp view of the semantic structure underlying the scientific literature. For this visualization to be understandable the complexity of the citation network must be reduced through an algorithm. This paper describes the Citation Pathfinder application and its integration into a prototype digital library. This application generates small-scale citation networks that expand upon the search results of the digital library. These domain maps are linked to the collection, creating an interface that is based on the communication patterns in science. The Main Path Analysis technique is employed to simplify these networks into linear, sequential structures. By identifying patterns that characterize the evolution of the research field, Citation Pathfinder uses citations to give users a deeper understanding of the scientific literature.

Frequency domain technique for a two-dimensional mapping of optical tissue properties

NASA Astrophysics Data System (ADS)

Bocher, Thomas; Beuthan, Juergen; Minet, Olaf; Naber, Rolf-Dieter; Mueller, Gerhard J.

1995-12-01

Locally and individually varying optical tissue parameters (mu) a, (mu) s, and g are responsible for non-neglectible uncertainties in the interpretation of spectroscopic data in optical biopsy techniques. The intrinsic fluorescence signal for instance doesn't depend only on the fluorophore concentration but also on the amount of other background absorbers and on alterations of scattering properties. Therefore neither a correct relative nor an absolute mapping of the lateral fluorophore concentration can be derived from the intrinsic fluorescence signal alone. Using MC-simulations it can be shown that in time-resolved LIFS the simultaneously measured backscattered signal of the excitation wavelength (UV) can be used to develop a special, linearized rescaling algorithm to take into account the most dominant of these varying tissue parameters which is (mu) a,ex. In combination with biochemical calibration measurements we were able to perform fiberbased quantitative NADH- concentration measurements. In this paper a new rescaling method for VIS and IR light in the frequency domain is proposed. It can be applied within the validity range of the diffusion approximation and provides full (mu) a and (mu) s rescaling possibility in a 2- dimensional, non-contact mapping mode. The scanning device is planned to be used in combination with a standard operation microscope of ZEISS, Germany.

The frequency-domain approach for apparent density mapping

NASA Astrophysics Data System (ADS)

Tong, T.; Guo, L.

2017-12-01

Apparent density mapping is a technique to estimate density distribution in the subsurface layer from the observed gravity data. It has been widely applied for geologic mapping, tectonic study and mineral exploration for decades. Apparent density mapping usually models the density layer as a collection of vertical, juxtaposed prisms in both horizontal directions, whose top and bottom surfaces are assumed to be horizontal or variable-depth, and then inverts or deconvolves the gravity anomalies to determine the density of each prism. Conventionally, the frequency-domain approach, which assumes that both top and bottom surfaces of the layer are horizontal, is usually utilized for fast density mapping. However, such assumption is not always valid in the real world, since either the top surface or the bottom surface may be variable-depth. Here, we presented a frequency-domain approach for apparent density mapping, which permits both the top and bottom surfaces of the layer to be variable-depth. We first derived the formula for forward calculation of gravity anomalies caused by the density layer, whose top and bottom surfaces are variable-depth, and the formula for inversion of gravity anomalies for the density distribution. Then we proposed the procedure for density mapping based on both the formulas of inversion and forward calculation. We tested the approach on the synthetic data, which verified its effectiveness. We also tested the approach on the real Bouguer gravity anomalies data from the central South China. The top surface was assumed to be flat and was on the sea level, and the bottom surface was considered as the Moho surface. The result presented the crustal density distribution, which was coinciding well with the basic tectonic features in the study area.

Characterizing the local optoelectronic performance of organic solar cells with scanning-probe microscopy

NASA Astrophysics Data System (ADS)

Coffey, David C.

2007-12-01

Conjugated polymers, small molecules, and colloidal semiconductor nanocrystals are promising materials for use in low-cost, thin-film solar cells. The photovoltaic performance of these materials, however, is highly dependent on film structure, and directly correlating local film structures with device performance remains challenging. This dissertation describes several techniques we have developed to probe and control the local optoelectronic properties of organic semiconducting films. First, with an aim of rapidly fabricating photovoltaic films with varying morphology, we demonstrate that Dip-Pen Nanolithography (DPN) can be used to control nanoscale phase separation with sub-150 nm lateral resolution in polymer films that are 20--80 nm thick. This control is based on writing monolayer chemical templates that nucleate phase separation, and we use this technique to study heterogeneous nucleation in thin films. Second, we use time-resolved electrostatic force microscopy (trEFM) to measure photoexcited charge in polymer films with a resolution of 100 nm and 100 mus. We show that such data can predict the external quantum efficiencies of polymer photodiodes, and can thus link device performance with local optoelectronic properties. When applied to the study of blended polyfluorene films, we show that domain centers can buildup charge faster then domain interfaces, which indicates that polymer/polymer blend devices should be modeled as having impure donor/acceptor domains. Third, we use photoconductive atomic force microscopy (pcAFM) to map local photocurrents with 20 nm-resolution in polymer/fullerene solar cells- achieving an order of magnitude better resolution than previous techniques. We present photocurrent maps under short-circuit conditions (zero applied bias), as well as under various applied voltages. We find significant variations in the short-circuit current between regions that appear identical in AFM topography. These variations occur from one domain to another, as well as on larger length scales incorporating multiple domains. Our results suggest that organic solar cells can be significantly improved with better donor/acceptor structuring.

Using Dynamic Contrast Enhanced MRI to Quantitatively Characterize Maternal Vascular Organization in the Primate Placenta

PubMed Central

Frias, A.E.; Schabel, M.C.; Roberts, V.H.J.; Tudorica, A.; Grigsby, P.L.; Oh, K.Y.; Kroenke, C. D.

2015-01-01

Purpose The maternal microvasculature of the primate placenta is organized into 10-20 perfusion domains that are functionally optimized to facilitate nutrient exchange to support fetal growth. This study describes a dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) method for identifying vascular domains, and quantifying maternal blood flow in them. Methods A rhesus macaque on the 133rd day of pregnancy (G133, term=165 days) underwent Doppler ultrasound (US) procedures, DCE-MRI, and Cesarean-section delivery. Serial T1-weighted images acquired throughout intravenous injection of a contrast reagent (CR) bolus were analyzed to obtain CR arrival time maps of the placenta. Results Watershed segmentation of the arrival time map identified 16 perfusion domains. The number and location of these domains corresponded to anatomical cotyledonary units observed following delivery. Analysis of the CR wave front through each perfusion domain enabled determination of volumetric flow, which ranged from 9.03 to 44.9 mL/sec (25.2 ± 10.3 mL/sec). These estimates are supported by Doppler US results. Conclusions The DCE-MRI analysis described here provides quantitative estimates of the number of maternal perfusion domains in a primate placenta, and estimates flow within each domain. Anticipated extensions of this technique are to the study placental function in nonhuman primate models of obstetric complications. PMID:24753177

Three-dimensional digital mapping of the optic nerve head cupping in glaucoma

NASA Astrophysics Data System (ADS)

Mitra, Sunanda; Ramirez, Manuel; Morales, Jose

1992-08-01

Visualization of the optic nerve head cupping is clinically achieved by stereoscopic viewing of a fundus image pair of the suspected eye. A novel algorithm for three-dimensional digital surface representation of the optic nerve head, using fusion of stereo depth map with a linearly stretched intensity image of a stereo fundus image pair, is presented. Prior to depth map acquisition, a number of preprocessing tasks including feature extraction, registration by cepstral analysis, and correction for intensity variations are performed. The depth map is obtained by using a coarse to fine strategy for obtaining disparities between corresponding areas. The required matching techniques to obtain the translational differences in every step, uses cepstral analysis and correlation-like scanning technique in the spatial domain for the finest details. The quantitative and precise representation of the optic nerve head surface topography following this algorithm is not computationally intensive and should provide more useful information than just qualitative stereoscopic viewing of the fundus as one of the diagnostic criteria for diagnosis of glaucoma.

The Scenario-Based Engineering Process (SEP): a user-centered approach for the development of health care systems.

PubMed

Harbison, K; Kelly, J; Burnell, L; Silva, J

1995-01-01

The Scenario-based Engineering Process (SEP) is a user-focused methodology for large and complex system design. This process supports new application development from requirements analysis with domain models to component selection, design and modification, implementation, integration, and archival placement. It is built upon object-oriented methodologies, domain modeling strategies, and scenario-based techniques to provide an analysis process for mapping application requirements to available components. We are using SEP in the health care applications that we are developing. The process has already achieved success in the manufacturing and military domains and is being adopted by many organizations. SEP should prove viable in any domain containing scenarios that can be decomposed into tasks.

Numerical time-domain electromagnetics based on finite-difference and convolution

NASA Astrophysics Data System (ADS)

Lin, Yuanqu

Time-domain methods posses a number of advantages over their frequency-domain counterparts for the solution of wideband, nonlinear, and time varying electromagnetic scattering and radiation phenomenon. Time domain integral equation (TDIE)-based methods, which incorporate the beneficial properties of integral equation method, are thus well suited for solving broadband scattering problems for homogeneous scatterers. Widespread adoption of TDIE solvers has been retarded relative to other techniques by their inefficiency, inaccuracy and instability. Moreover, two-dimensional (2D) problems are especially problematic, because 2D Green's functions have infinite temporal support, exacerbating these difficulties. This thesis proposes a finite difference delay modeling (FDDM) scheme for the solution of the integral equations of 2D transient electromagnetic scattering problems. The method discretizes the integral equations temporally using first- and second-order finite differences to map Laplace-domain equations into the Z domain before transforming to the discrete time domain. The resulting procedure is unconditionally stable because of the nature of the Laplace- to Z-domain mapping. The first FDDM method developed in this thesis uses second-order Lagrange basis functions with Galerkin's method for spatial discretization. The second application of the FDDM method discretizes the space using a locally-corrected Nystrom method, which accelerates the precomputation phase and achieves high order accuracy. The Fast Fourier Transform (FFT) is applied to accelerate the marching-on-time process in both methods. While FDDM methods demonstrate impressive accuracy and stability in solving wideband scattering problems for homogeneous scatterers, they still have limitations in analyzing interactions between several inhomogenous scatterers. Therefore, this thesis devises a multi-region finite-difference time-domain (MR-FDTD) scheme based on domain-optimal Green's functions for solving sparsely-populated problems. The scheme uses a discrete Green's function (DGF) on the FDTD lattice to truncate the local subregions, and thus reduces reflection error on the local boundary. A continuous Green's function (CGF) is implemented to pass the influence of external fields into each FDTD region which mitigates the numerical dispersion and anisotropy of standard FDTD. Numerical results will illustrate the accuracy and stability of the proposed techniques.

Self-Organizing Hidden Markov Model Map (SOHMMM): Biological Sequence Clustering and Cluster Visualization.

PubMed

Ferles, Christos; Beaufort, William-Scott; Ferle, Vanessa

2017-01-01

The present study devises mapping methodologies and projection techniques that visualize and demonstrate biological sequence data clustering results. The Sequence Data Density Display (SDDD) and Sequence Likelihood Projection (SLP) visualizations represent the input symbolical sequences in a lower-dimensional space in such a way that the clusters and relations of data elements are depicted graphically. Both operate in combination/synergy with the Self-Organizing Hidden Markov Model Map (SOHMMM). The resulting unified framework is in position to analyze automatically and directly raw sequence data. This analysis is carried out with little, or even complete absence of, prior information/domain knowledge.

Doping profile measurements in silicon using terahertz time domain spectroscopy (THz-TDS) via electrochemical anodic oxidation

NASA Astrophysics Data System (ADS)

Tulsyan, Gaurav

Doping profiles are engineered to manipulate device properties and to determine electrical performances of microelectronic devices frequently. To support engineering studies afterward, essential information is usually required from physically characterized doping profiles. Secondary Ion Mass Spectrometry (SIMS), Spreading Resistance Profiling (SRP) and Electrochemical Capacitance Voltage (ECV) profiling are standard techniques for now to map profile. SIMS yields a chemical doping profile via ion sputtering process and owns a better resolution, whereas ECV and SRP produce an electrical doping profile detecting free carriers in microelectronic devices. The major difference between electrical and chemical doping profiles is at heavily doped regions greater than 1020 atoms/cm3. At the profile region over the solubility limit, inactive dopants induce a flat plateau and detected by electrical measurements only. Destructive techniques are usually designed as stand-alone systems to study impurities. For an in-situ process control purpose, non-contact methods, such as ellipsometry and non-contact capacitance voltage (CV) techniques are current under development. In this theses work, terahertz time domain spectroscopy (THz-TDS) is utilized to achieve electrical doping profile in both destructive and non-contact manners. In recent years the Terahertz group at Rochester Institute Technology developed several techniques that use terahertz pulses to non-destructively map doping profiles. In this thesis, we study a destructive but potentially higher resolution version of the terahertz based approach to map the profile of activated dopants and augment the non-destructive approaches already developed. The basic idea of the profile mapping approach developed in this MS thesis is to anodize, and thus oxidize to silicon dioxide, thin layers (down to below 10 nm) of the wafer with the doping profile to be mapped. Since the dopants atoms and any free carriers in the silicon oxide thin film are invisible to the terahertz probe this anodization step very effectively removes a 'thin slice' from the doping profile to be mapped. By iterating between anodization and terahertz measurements that detect only the 'remaining' non-oxidized portion of the doping profile one can re-construct the doping profile with significantly higher precision compared to what is possible by only a single non-destructive measurement of the un-anodized profile as used in the non-destructive version of our technique. In this MS thesis we explore all aspects of this anodization based variation of doping profile mapping using free space terahertz pulses. This includes a study of silicon dioxide thin film growth using a room temperature electrochemical oxidation process. Etching procedures providing the option to remove between successive anodization and terahertz measurement steps. THz-TDS measurements of successively anodized profiles will be compared with sheet resistance and SIMS measurements to benchmark and improve the new technique.

Automatic segmentation of closed-contour features in ophthalmic images using graph theory and dynamic programming.

PubMed

Chiu, Stephanie J; Toth, Cynthia A; Bowes Rickman, Catherine; Izatt, Joseph A; Farsiu, Sina

2012-05-01

This paper presents a generalized framework for segmenting closed-contour anatomical and pathological features using graph theory and dynamic programming (GTDP). More specifically, the GTDP method previously developed for quantifying retinal and corneal layer thicknesses is extended to segment objects such as cells and cysts. The presented technique relies on a transform that maps closed-contour features in the Cartesian domain into lines in the quasi-polar domain. The features of interest are then segmented as layers via GTDP. Application of this method to segment closed-contour features in several ophthalmic image types is shown. Quantitative validation experiments for retinal pigmented epithelium cell segmentation in confocal fluorescence microscopy images attests to the accuracy of the presented technique.

Automatic segmentation of closed-contour features in ophthalmic images using graph theory and dynamic programming

PubMed Central

Chiu, Stephanie J.; Toth, Cynthia A.; Bowes Rickman, Catherine; Izatt, Joseph A.; Farsiu, Sina

2012-01-01

This paper presents a generalized framework for segmenting closed-contour anatomical and pathological features using graph theory and dynamic programming (GTDP). More specifically, the GTDP method previously developed for quantifying retinal and corneal layer thicknesses is extended to segment objects such as cells and cysts. The presented technique relies on a transform that maps closed-contour features in the Cartesian domain into lines in the quasi-polar domain. The features of interest are then segmented as layers via GTDP. Application of this method to segment closed-contour features in several ophthalmic image types is shown. Quantitative validation experiments for retinal pigmented epithelium cell segmentation in confocal fluorescence microscopy images attests to the accuracy of the presented technique. PMID:22567602

Fast tracking the design of theory-based KT interventions through a consensus process.

PubMed

Bussières, André E; Al Zoubi, Fadi; Quon, Jeffrey A; Ahmed, Sara; Thomas, Aliki; Stuber, Kent; Sajko, Sandy; French, Simon

2015-02-11

Despite available evidence for optimal management of spinal pain, poor adherence to guidelines and wide variations in healthcare services persist. One of the objectives of the Canadian Chiropractic Guideline Initiative is to develop and evaluate targeted theory- and evidence-informed interventions to improve the management of non-specific neck pain by chiropractors. In order to systematically develop a knowledge translation (KT) intervention underpinned by the Theoretical Domains Framework (TDF), we explored the factors perceived to influence the use of multimodal care to manage non-specific neck pain, and mapped behaviour change techniques to key theoretical domains. Individual telephone interviews exploring beliefs about managing neck pain were conducted with a purposive sample of 13 chiropractors. The interview guide was based upon the TDF. Interviews were digitally recorded, transcribed verbatim and analysed by two independent assessors using thematic content analysis. A 15-member expert panel formally met to design a KT intervention. Nine TDF domains were identified as likely relevant. Key beliefs (and relevant domains of the TDF) included the following: influence of formal training, colleagues and patients on clinicians (Social Influences); availability of educational material (Environmental Context and Resources); and better clinical outcomes reinforcing the use of multimodal care (Reinforcement). Facilitating factors considered important included better communication (Skills); audits of patients' treatment-related outcomes (Behavioural Regulation); awareness and agreement with guidelines (Knowledge); and tailoring of multimodal care (Memory, Attention and Decision Processes). Clinicians conveyed conflicting beliefs about perceived threats to professional autonomy (Social/Professional Role and Identity) and speed of recovery from either applying or ignoring the practice recommendations (Beliefs about Consequences). The expert panel mapped behaviour change techniques to key theoretical domains and identified relevant KT strategies and modes of delivery to increase the use of multimodal care among chiropractors. A multifaceted KT educational intervention targeting chiropractors' management of neck pain was developed. The KT intervention consisted of an online education webinar series, clinical vignettes and a video underpinned by the Brief Action Planning model. The intervention was designed to reflect key theoretical domains, behaviour change techniques and intervention components. The effectiveness of the proposed intervention remains to be tested.

Cross-domain question classification in community question answering via kernel mapping

NASA Astrophysics Data System (ADS)

Su, Lei; Hu, Zuoliang; Yang, Bin; Li, Yiyang; Chen, Jun

2015-10-01

An increasingly popular method for retrieving information is via the community question answering (CQA) systems such as Yahoo! Answers and Baidu Knows. In CQA, question classification plays an important role to find the answers. However, the labeled training examples for statistical question classifier are fairly expensive to obtain, as they require the experienced human efforts. Meanwhile, unlabeled data are readily available. This paper employs the method of domain adaptation via kernel mapping to solve this problem. In detail, the kernel approach is utilized to map the target-domain data and the source-domain data into a common space, where the question classifiers are trained under the closer conditional probabilities. The kernel mapping function is constructed by domain knowledge. Therefore, domain knowledge could be transferred from the labeled examples in the source domain to the unlabeled ones in the targeted domain. The statistical training model can be improved by using a large number of unlabeled data. Meanwhile, the Hadoop Platform is used to construct the mapping mechanism to reduce the time complexity. Map/Reduce enable kernel mapping for domain adaptation in parallel in the Hadoop Platform. Experimental results show that the accuracy of question classification could be improved by the method of kernel mapping. Furthermore, the parallel method in the Hadoop Platform could effective schedule the computing resources to reduce the running time.

Deep nets vs expert designed features in medical physics: An IMRT QA case study.

PubMed

Interian, Yannet; Rideout, Vincent; Kearney, Vasant P; Gennatas, Efstathios; Morin, Olivier; Cheung, Joey; Solberg, Timothy; Valdes, Gilmer

2018-03-30

The purpose of this study was to compare the performance of Deep Neural Networks against a technique designed by domain experts in the prediction of gamma passing rates for Intensity Modulated Radiation Therapy Quality Assurance (IMRT QA). A total of 498 IMRT plans across all treatment sites were planned in Eclipse version 11 and delivered using a dynamic sliding window technique on Clinac iX or TrueBeam Linacs. Measurements were performed using a commercial 2D diode array, and passing rates for 3%/3 mm local dose/distance-to-agreement (DTA) were recorded. Separately, fluence maps calculated for each plan were used as inputs to a convolution neural network (CNN). The CNNs were trained to predict IMRT QA gamma passing rates using TensorFlow and Keras. A set of model architectures, inspired by the convolutional blocks of the VGG-16 ImageNet model, were constructed and implemented. Synthetic data, created by rotating and translating the fluence maps during training, was created to boost the performance of the CNNs. Dropout, batch normalization, and data augmentation were utilized to help train the model. The performance of the CNNs was compared to a generalized Poisson regression model, previously developed for this application, which used 78 expert designed features. Deep Neural Networks without domain knowledge achieved comparable performance to a baseline system designed by domain experts in the prediction of 3%/3 mm Local gamma passing rates. An ensemble of neural nets resulted in a mean absolute error (MAE) of 0.70 ± 0.05 and the domain expert model resulted in a 0.74 ± 0.06. Convolutional neural networks (CNNs) with transfer learning can predict IMRT QA passing rates by automatically designing features from the fluence maps without human expert supervision. Predictions from CNNs are comparable to a system carefully designed by physicist experts. © 2018 American Association of Physicists in Medicine.

Generalization of the Schwarz–Christoffel mapping to multiply connected polygonal domains

PubMed Central

Vasconcelos, Giovani L.

2014-01-01

A generalization of the Schwarz–Christoffel mapping to multiply connected polygonal domains is obtained by making a combined use of two preimage domains, namely, a rectilinear slit domain and a bounded circular domain. The conformal mapping from the circular domain to the polygonal region is written as an indefinite integral whose integrand consists of a product of powers of the Schottky-Klein prime functions, which is the same irrespective of the preimage slit domain, and a prefactor function that depends on the choice of the rectilinear slit domain. A detailed derivation of the mapping formula is given for the case where the preimage slit domain is the upper half-plane with radial slits. Representation formulae for other canonical slit domains are also obtained but they are more cumbersome in that the prefactor function contains arbitrary parameters in the interior of the circular domain. PMID:24910523

Generalization of the Schwarz-Christoffel mapping to multiply connected polygonal domains.

PubMed

Vasconcelos, Giovani L

2014-06-08

A generalization of the Schwarz-Christoffel mapping to multiply connected polygonal domains is obtained by making a combined use of two preimage domains, namely, a rectilinear slit domain and a bounded circular domain. The conformal mapping from the circular domain to the polygonal region is written as an indefinite integral whose integrand consists of a product of powers of the Schottky-Klein prime functions, which is the same irrespective of the preimage slit domain, and a prefactor function that depends on the choice of the rectilinear slit domain. A detailed derivation of the mapping formula is given for the case where the preimage slit domain is the upper half-plane with radial slits. Representation formulae for other canonical slit domains are also obtained but they are more cumbersome in that the prefactor function contains arbitrary parameters in the interior of the circular domain.

Diffuse ultrasound monitoring of stress and damage development on a 15-ton concrete beam.

PubMed

Zhang, Yuxiang; Planès, Thomas; Larose, Eric; Obermann, Anne; Rospars, Claude; Moreau, Gautier

2016-04-01

This paper describes the use of an ultrasonic imaging technique (Locadiff) for the Non-Destructive Testing & Evaluation of a concrete structure. By combining coda wave interferometry and a sensitivity kernel for diffuse waves, Locadiff can monitor the elastic and structural properties of a heterogeneous material with a high sensitivity, and can map changes of these properties over time when a perturbation occurs in the bulk of the material. The applicability of the technique to life-size concrete structures is demonstrated through the monitoring of a 15-ton reinforced concrete beam subject to a four-point bending test causing cracking. The experimental results show that Locadiff achieved to (1) detect and locate the cracking zones in the core of the concrete beam at an early stage by mapping the changes in the concrete's micro-structure; (2) monitor the internal stress level in both temporal and spatial domains by mapping the variation in velocity caused by the acousto-elastic effect. The mechanical behavior of the concrete structure is also studied using conventional techniques such as acoustic emission, vibrating wire extensometers, and digital image correlation. The performances of the Locadiff technique in the detection of early stage cracking are assessed and discussed.

Mining e-Learning Domain Concept Map from Academic Articles

ERIC Educational Resources Information Center

Chen, Nian-Shing; Kinshuk; Wei, Chun-Wang; Chen, Hong-Jhe

2008-01-01

Recent researches have demonstrated the importance of concept map and its versatile applications especially in e-Learning. For example, while designing adaptive learning materials, designers need to refer to the concept map of a subject domain. Moreover, concept maps can show the whole picture and core knowledge about a subject domain. Research…

Gradient-based multiresolution image fusion.

PubMed

Petrović, Valdimir S; Xydeas, Costas S

2004-02-01

A novel approach to multiresolution signal-level image fusion is presented for accurately transferring visual information from any number of input image signals, into a single fused image without loss of information or the introduction of distortion. The proposed system uses a "fuse-then-decompose" technique realized through a novel, fusion/decomposition system architecture. In particular, information fusion is performed on a multiresolution gradient map representation domain of image signal information. At each resolution, input images are represented as gradient maps and combined to produce new, fused gradient maps. Fused gradient map signals are processed, using gradient filters derived from high-pass quadrature mirror filters to yield a fused multiresolution pyramid representation. The fused output image is obtained by applying, on the fused pyramid, a reconstruction process that is analogous to that of conventional discrete wavelet transform. This new gradient fusion significantly reduces the amount of distortion artefacts and the loss of contrast information usually observed in fused images obtained from conventional multiresolution fusion schemes. This is because fusion in the gradient map domain significantly improves the reliability of the feature selection and information fusion processes. Fusion performance is evaluated through informal visual inspection and subjective psychometric preference tests, as well as objective fusion performance measurements. Results clearly demonstrate the superiority of this new approach when compared to conventional fusion systems.

Intra-operative multi-site stimulation: Expanding methodology for cortical brain mapping of language functions

PubMed Central

Korn, Akiva; Kirschner, Adi; Perry, Daniella; Hendler, Talma; Ram, Zvi

2017-01-01

Direct cortical stimulation (DCS) is considered the gold-standard for functional cortical mapping during awake surgery for brain tumor resection. DCS is performed by stimulating one local cortical area at a time. We present a feasibility study using an intra-operative technique aimed at improving our ability to map brain functions which rely on activity in distributed cortical regions. Following standard DCS, Multi-Site Stimulation (MSS) was performed in 15 patients by applying simultaneous cortical stimulations at multiple locations. Language functioning was chosen as a case-cognitive domain due to its relatively well-known cortical organization. MSS, performed at sites that did not produce disruption when applied in a single stimulation point, revealed additional language dysfunction in 73% of the patients. Functional regions identified by this technique were presumed to be significant to language circuitry and were spared during surgery. No new neurological deficits were observed in any of the patients following surgery. Though the neuro-electrical effects of MSS need further investigation, this feasibility study may provide a first step towards sophistication of intra-operative cortical mapping. PMID:28700619

Intra-operative multi-site stimulation: Expanding methodology for cortical brain mapping of language functions.

PubMed

Gonen, Tal; Gazit, Tomer; Korn, Akiva; Kirschner, Adi; Perry, Daniella; Hendler, Talma; Ram, Zvi

2017-01-01

Direct cortical stimulation (DCS) is considered the gold-standard for functional cortical mapping during awake surgery for brain tumor resection. DCS is performed by stimulating one local cortical area at a time. We present a feasibility study using an intra-operative technique aimed at improving our ability to map brain functions which rely on activity in distributed cortical regions. Following standard DCS, Multi-Site Stimulation (MSS) was performed in 15 patients by applying simultaneous cortical stimulations at multiple locations. Language functioning was chosen as a case-cognitive domain due to its relatively well-known cortical organization. MSS, performed at sites that did not produce disruption when applied in a single stimulation point, revealed additional language dysfunction in 73% of the patients. Functional regions identified by this technique were presumed to be significant to language circuitry and were spared during surgery. No new neurological deficits were observed in any of the patients following surgery. Though the neuro-electrical effects of MSS need further investigation, this feasibility study may provide a first step towards sophistication of intra-operative cortical mapping.

Parallel mapping of optical near-field interactions by molecular motor-driven quantum dots.

PubMed

Groß, Heiko; Heil, Hannah S; Ehrig, Jens; Schwarz, Friedrich W; Hecht, Bert; Diez, Stefan

2018-04-30

In the vicinity of metallic nanostructures, absorption and emission rates of optical emitters can be modulated by several orders of magnitude 1,2 . Control of such near-field light-matter interaction is essential for applications in biosensing 3 , light harvesting 4 and quantum communication 5,6 and requires precise mapping of optical near-field interactions, for which single-emitter probes are promising candidates 7-11 . However, currently available techniques are limited in terms of throughput, resolution and/or non-invasiveness. Here, we present an approach for the parallel mapping of optical near-field interactions with a resolution of <5 nm using surface-bound motor proteins to transport microtubules carrying single emitters (quantum dots). The deterministic motion of the quantum dots allows for the interpolation of their tracked positions, resulting in an increased spatial resolution and a suppression of localization artefacts. We apply this method to map the near-field distribution of nanoslits engraved into gold layers and find an excellent agreement with finite-difference time-domain simulations. Our technique can be readily applied to a variety of surfaces for scalable, nanometre-resolved and artefact-free near-field mapping using conventional wide-field microscopes.

Exponential convergence through linear finite element discretization of stratified subdomains

NASA Astrophysics Data System (ADS)

Guddati, Murthy N.; Druskin, Vladimir; Vaziri Astaneh, Ali

2016-10-01

Motivated by problems where the response is needed at select localized regions in a large computational domain, we devise a novel finite element discretization that results in exponential convergence at pre-selected points. The key features of the discretization are (a) use of midpoint integration to evaluate the contribution matrices, and (b) an unconventional mapping of the mesh into complex space. Named complex-length finite element method (CFEM), the technique is linked to Padé approximants that provide exponential convergence of the Dirichlet-to-Neumann maps and thus the solution at specified points in the domain. Exponential convergence facilitates drastic reduction in the number of elements. This, combined with sparse computation associated with linear finite elements, results in significant reduction in the computational cost. The paper presents the basic ideas of the method as well as illustration of its effectiveness for a variety of problems involving Laplace, Helmholtz and elastodynamics equations.

Functional feature embedded space mapping of fMRI data.

PubMed

Hu, Jin; Tian, Jie; Yang, Lei

2006-01-01

We have proposed a new method for fMRI data analysis which is called Functional Feature Embedded Space Mapping (FFESM). Our work mainly focuses on the experimental design with periodic stimuli which can be described by a number of Fourier coefficients in the frequency domain. A nonlinear dimension reduction technique Isomap is applied to the high dimensional features obtained from frequency domain of the fMRI data for the first time. Finally, the presence of activated time series is identified by the clustering method in which the information theoretic criterion of minimum description length (MDL) is used to estimate the number of clusters. The feasibility of our algorithm is demonstrated by real human experiments. Although we focus on analyzing periodic fMRI data, the approach can be extended to analyze non-periodic fMRI data (event-related fMRI) by replacing the Fourier analysis with a wavelet analysis.

A Review of Depth and Normal Fusion Algorithms

PubMed Central

Štolc, Svorad; Pock, Thomas

2018-01-01

Geometric surface information such as depth maps and surface normals can be acquired by various methods such as stereo light fields, shape from shading and photometric stereo techniques. We compare several algorithms which deal with the combination of depth with surface normal information in order to reconstruct a refined depth map. The reasons for performance differences are examined from the perspective of alternative formulations of surface normals for depth reconstruction. We review and analyze methods in a systematic way. Based on our findings, we introduce a new generalized fusion method, which is formulated as a least squares problem and outperforms previous methods in the depth error domain by introducing a novel normal weighting that performs closer to the geodesic distance measure. Furthermore, a novel method is introduced based on Total Generalized Variation (TGV) which further outperforms previous approaches in terms of the geodesic normal distance error and maintains comparable quality in the depth error domain. PMID:29389903

A Chebyshev matrix method for spatial modes of the Orr-Sommerfeld equation

NASA Technical Reports Server (NTRS)

Danabasoglu, G.; Biringen, S.

1989-01-01

The Chebyshev matrix collocation method is applied to obtain the spatial modes of the Orr-Sommerfeld equation for Poiseuille flow and the Blausius boundary layer. The problem is linearized by the companion matrix technique for semi-infinite domain using a mapping transformation. The method can be easily adapted to problems with different boundary conditions requiring different transformations.

3D Mapping of Language Networks in Clinical and Pre-Clinical Alzheimer's Disease

ERIC Educational Resources Information Center

Apostolova, Liana G.; Lu, Po; Rogers, Steve; Dutton, Rebecca A.; Hayashi, Kiralee M.; Toga, Arthur W.; Cummings, Jeffrey L.; Thompson, Paul M.

2008-01-01

We investigated the associations between Boston naming and the animal fluency tests and cortical atrophy in 19 probable AD and 5 multiple domain amnestic mild cognitive impairment patients who later converted to AD. We applied a surface-based computational anatomy technique to MRI scans of the brain and then used linear regression models to detect…

Monitoring urban tree cover using object-based image analysis and public domain remotely sensed data

Treesearch

L. Monika Moskal; Diane M. Styers; Meghan Halabisky

2011-01-01

Urban forest ecosystems provide a range of social and ecological services, but due to the heterogeneity of these canopies their spatial extent is difficult to quantify and monitor. Traditional per-pixel classification methods have been used to map urban canopies, however, such techniques are not generally appropriate for assessing these highly variable landscapes....

Sequence-structure mapping errors in the PDB: OB-fold domains

PubMed Central

Venclovas, Česlovas; Ginalski, Krzysztof; Kang, Chulhee

2004-01-01

The Protein Data Bank (PDB) is the single most important repository of structural data for proteins and other biologically relevant molecules. Therefore, it is critically important to keep the PDB data, as much as possible, error-free. In this study, we have analyzed PDB crystal structures possessing oligonucleotide/oligosaccharide binding (OB)-fold, one of the highly populated folds, for the presence of sequence-structure mapping errors. Using energy-based structure quality assessment coupled with sequence analyses, we have found that there are at least five OB-structures in the PDB that have regions where sequences have been incorrectly mapped onto the structure. We have demonstrated that the combination of these computation techniques is effective not only in detecting sequence-structure mapping errors, but also in providing guidance to correct them. Namely, we have used results of computational analysis to direct a revision of X-ray data for one of the PDB entries containing a fairly inconspicuous sequence-structure mapping error. The revised structure has been deposited with the PDB. We suggest use of computational energy assessment and sequence analysis techniques to facilitate structure determination when homologs having known structure are available to use as a reference. Such computational analysis may be useful in either guiding the sequence-structure assignment process or verifying the sequence mapping within poorly defined regions. PMID:15133161

Spatiotemporal mapping of scalp potentials.

PubMed

Fender, D H; Santoro, T P

1977-11-01

Computerized analysis and display techniques are applied to the problem of identifying the origins of visually evoked scalped potentials (VESP's). A new stimulus for VESP work, white noise, is being incorporated in the solution of this problem. VESP's for white-noise stimulation exhibit time domain behavior similar to the classical response for flash stimuli but with certain significant differences. Contour mapping algorithms are used to display the time behavior of equipotential surfaces on the scalp during the VESP. The electrical and geometrical parameters of the head are modeled. Electrical fields closely matching those obtained experimentally are generated on the surface of the model head by optimally selecting the location and strength parameters of one or two dipole current sources contained within the model. Computer graphics are used to display as a movie the actual and model scalp potential field and the parameters of the dipole generators whithin the model head during the time course of the VESP. These techniques are currently used to study retinotopic mapping, fusion, and texture perception in the human.

Time-distance domain transformation for Acoustic Emission source localization in thin metallic plates.

PubMed

Grabowski, Krzysztof; Gawronski, Mateusz; Baran, Ireneusz; Spychalski, Wojciech; Staszewski, Wieslaw J; Uhl, Tadeusz; Kundu, Tribikram; Packo, Pawel

2016-05-01

Acoustic Emission used in Non-Destructive Testing is focused on analysis of elastic waves propagating in mechanical structures. Then any information carried by generated acoustic waves, further recorded by a set of transducers, allow to determine integrity of these structures. It is clear that material properties and geometry strongly impacts the result. In this paper a method for Acoustic Emission source localization in thin plates is presented. The approach is based on the Time-Distance Domain Transform, that is a wavenumber-frequency mapping technique for precise event localization. The major advantage of the technique is dispersion compensation through a phase-shifting of investigated waveforms in order to acquire the most accurate output, allowing for source-sensor distance estimation using a single transducer. The accuracy and robustness of the above process are also investigated. This includes the study of Young's modulus value and numerical parameters influence on damage detection. By merging the Time-Distance Domain Transform with an optimal distance selection technique, an identification-localization algorithm is achieved. The method is investigated analytically, numerically and experimentally. The latter involves both laboratory and large scale industrial tests. Copyright © 2016 Elsevier B.V. All rights reserved.

Chaotic CDMA watermarking algorithm for digital image in FRFT domain

NASA Astrophysics Data System (ADS)

Liu, Weizhong; Yang, Wentao; Feng, Zhuoming; Zou, Xuecheng

2007-11-01

A digital image-watermarking algorithm based on fractional Fourier transform (FRFT) domain is presented by utilizing chaotic CDMA technique in this paper. As a popular and typical transmission technique, CDMA has many advantages such as privacy, anti-jamming and low power spectral density, which can provide robustness against image distortions and malicious attempts to remove or tamper with the watermark. A super-hybrid chaotic map, with good auto-correlation and cross-correlation characteristics, is adopted to produce many quasi-orthogonal codes (QOC) that can replace the periodic PN-code used in traditional CDAM system. The watermarking data is divided into a lot of segments that correspond to different chaotic QOC respectively and are modulated into the CDMA watermarking data embedded into low-frequency amplitude coefficients of FRFT domain of the cover image. During watermark detection, each chaotic QOC extracts its corresponding watermarking segment by calculating correlation coefficients between chaotic QOC and watermarked data of the detected image. The CDMA technique not only can enhance the robustness of watermark but also can compress the data of the modulated watermark. Experimental results show that the watermarking algorithm has good performances in three aspects: better imperceptibility, anti-attack robustness and security.

GPU-Based Interactive Exploration and Online Probability Maps Calculation for Visualizing Assimilated Ocean Ensembles Data

NASA Astrophysics Data System (ADS)

Hoteit, I.; Hollt, T.; Hadwiger, M.; Knio, O. M.; Gopalakrishnan, G.; Zhan, P.

2016-02-01

Ocean reanalyses and forecasts are nowadays generated by combining ensemble simulations with data assimilation techniques. Most of these techniques resample the ensemble members after each assimilation cycle. Tracking behavior over time, such as all possible paths of a particle in an ensemble vector field, becomes very difficult, as the number of combinations rises exponentially with the number of assimilation cycles. In general a single possible path is not of interest but only the probabilities that any point in space might be reached by a particle at some point in time. We present an approach using probability-weighted piecewise particle trajectories to allow for interactive probability mapping. This is achieved by binning the domain and splitting up the tracing process into the individual assimilation cycles, so that particles that fall into the same bin after a cycle can be treated as a single particle with a larger probability as input for the next cycle. As a result we loose the possibility to track individual particles, but can create probability maps for any desired seed at interactive rates. The technique is integrated in an interactive visualization system that enables the visual analysis of the particle traces side by side with other forecast variables, such as the sea surface height, and their corresponding behavior over time. By harnessing the power of modern graphics processing units (GPUs) for visualization as well as computation, our system allows the user to browse through the simulation ensembles in real-time, view specific parameter settings or simulation models and move between different spatial or temporal regions without delay. In addition our system provides advanced visualizations to highlight the uncertainty, or show the complete distribution of the simulations at user-defined positions over the complete time series of the domain.

The Synthesis Map Is a Multidimensional Educational Tool That Provides Insight into Students’ Mental Models and Promotes Students’ Synthetic Knowledge Generation

PubMed Central

Ortega, Ryan A.; Brame, Cynthia J.

2015-01-01

Concept mapping was developed as a method of displaying and organizing hierarchical knowledge structures. Using the new, multidimensional presentation software Prezi, we have developed a new teaching technique designed to engage higher-level skills in the cognitive domain. This tool, synthesis mapping, is a natural evolution of concept mapping, which utilizes embedding to layer information within concepts. Prezi’s zooming user interface lets the author of the presentation use both depth as well as distance to show connections between data, ideas, and concepts. Students in the class Biology of Cancer created synthesis maps to illustrate their knowledge of tumorigenesis. Students used multiple organizational schemes to build their maps. We present an analysis of student work, placing special emphasis on organization within student maps and how the organization of knowledge structures in student maps can reveal strengths and weaknesses in student understanding or instruction. We also provide a discussion of best practices for instructors who would like to implement synthesis mapping in their classrooms. PMID:25917385

Space-time PM2.5 mapping in the severe haze region of Jing-Jin-Ji (China) using a synthetic approach.

PubMed

He, Junyu; Christakos, George

2018-05-07

Long- and short-term exposure to PM 2.5 is of great concern in China due to its adverse population health effects. Characteristic of the severity of the situation in China is that in the Jing-Jin-Ji region considered in this work a total of 2725 excess deaths have been attributed to short-term PM 2.5 exposure during the period January 10-31, 2013. Technically, the processing of large space-time PM 2.5 datasets and the mapping of the space-time distribution of PM 2.5 concentrations often constitute high-cost projects. To address this situation, we propose a synthetic modeling framework based on the integration of (a) the Bayesian maximum entropy method that assimilates auxiliary information from land-use regression and artificial neural network (ANN) model outputs based on PM 2.5 monitoring, satellite remote sensing data, land use and geographical records, with (b) a space-time projection technique that transforms the PM 2.5 concentration values from the original spatiotemporal domain onto a spatial domain that moves along the direction of the PM 2.5 velocity spread. An interesting methodological feature of the synthetic approach is that its components (methods or models) are complementary, i.e., one component can compensate for the occasional limitations of another component. Insight is gained in terms of a PM 2.5 case study covering the severe haze Jing-Jin-Ji region during October 1-31, 2015. The proposed synthetic approach explicitly accounted for physical space-time dependencies of the PM 2.5 distribution. Moreover, the assimilation of auxiliary information and the dimensionality reduction achieved by the synthetic approach produced rather impressive results: It generated PM 2.5 concentration maps with low estimation uncertainty (even at counties and villages far away from the monitoring stations, whereas during the haze periods the uncertainty reduction was over 50% compared to standard PM 2.5 mapping techniques); and it also proved to be computationally very efficient (the reduction in computational time was over 20% compared to standard mapping techniques). Copyright © 2018 Elsevier Ltd. All rights reserved.

The maps problem and the mapping problem: Two challenges for a cognitive neuroscience of speech and language

PubMed Central

Poeppel, David

2012-01-01

Research on the brain basis of speech and language faces theoretical and empirical challenges. The majority of current research, dominated by imaging, deficit-lesion, and electrophysiological techniques, seeks to identify regions that underpin aspects of language processing such as phonology, syntax, or semantics. The emphasis lies on localization and spatial characterization of function. The first part of the paper deals with a practical challenge that arises in the context of such a research program. This maps problem concerns the extent to which spatial information and localization can satisfy the explanatory needs for perception and cognition. Several areas of investigation exemplify how the neural basis of speech and language is discussed in those terms (regions, streams, hemispheres, networks). The second part of the paper turns to a more troublesome challenge, namely how to formulate the formal links between neurobiology and cognition. This principled problem thus addresses the relation between the primitives of cognition (here speech, language) and neurobiology. Dealing with this mapping problem invites the development of linking hypotheses between the domains. The cognitive sciences provide granular, theoretically motivated claims about the structure of various domains (the ‘cognome’); neurobiology, similarly, provides a list of the available neural structures. However, explanatory connections will require crafting computationally explicit linking hypotheses at the right level of abstraction. For both the practical maps problem and the principled mapping problem, developmental approaches and evidence can play a central role in the resolution. PMID:23017085

Moraxella catarrhalis synthesizes an autotransporter that is an acid phosphatase.

PubMed

Hoopman, Todd C; Wang, Wei; Brautigam, Chad A; Sedillo, Jennifer L; Reilly, Thomas J; Hansen, Eric J

2008-02-01

Moraxella catarrhalis O35E was shown to synthesize a 105-kDa protein that has similarity to both acid phosphatases and autotransporters. The N-terminal portion of the M. catarrhalis acid phosphatase A (MapA) was most similar (the BLAST probability score was 10(-10)) to bacterial class A nonspecific acid phosphatases. The central region of the MapA protein had similarity to passenger domains of other autotransporter proteins, whereas the C-terminal portion of MapA resembled the translocation domain of conventional autotransporters. Cloning and expression of the M. catarrhalis mapA gene in Escherichia coli confirmed the presence of acid phosphatase activity in the MapA protein. The MapA protein was shown to be localized to the outer membrane of M. catarrhalis and was not detected either in the soluble cytoplasmic fraction from disrupted M. catarrhalis cells or in the spent culture supernatant fluid from M. catarrhalis. Use of the predicted MapA translocation domain in a fusion construct with the passenger domain from another predicted M. catarrhalis autotransporter confirmed the translocation ability of this MapA domain. Inactivation of the mapA gene in M. catarrhalis strain O35E reduced the acid phosphatase activity expressed by this organism, and this mutation could be complemented in trans with the wild-type mapA gene. Nucleotide sequence analysis of the mapA gene from six M. catarrhalis strains showed that this protein was highly conserved among strains of this pathogen. Site-directed mutagenesis of a critical histidine residue (H233A) in the predicted active site of the acid phosphatase domain in MapA eliminated acid phosphatase activity in the recombinant MapA protein. This is the first description of an autotransporter protein that expresses acid phosphatase activity.

Moraxella catarrhalis Synthesizes an Autotransporter That Is an Acid Phosphatase▿

PubMed Central

Hoopman, Todd C.; Wang, Wei; Brautigam, Chad A.; Sedillo, Jennifer L.; Reilly, Thomas J.; Hansen, Eric J.

2008-01-01

Moraxella catarrhalis O35E was shown to synthesize a 105-kDa protein that has similarity to both acid phosphatases and autotransporters. The N-terminal portion of the M. catarrhalis acid phosphatase A (MapA) was most similar (the BLAST probability score was 10−10) to bacterial class A nonspecific acid phosphatases. The central region of the MapA protein had similarity to passenger domains of other autotransporter proteins, whereas the C-terminal portion of MapA resembled the translocation domain of conventional autotransporters. Cloning and expression of the M. catarrhalis mapA gene in Escherichia coli confirmed the presence of acid phosphatase activity in the MapA protein. The MapA protein was shown to be localized to the outer membrane of M. catarrhalis and was not detected either in the soluble cytoplasmic fraction from disrupted M. catarrhalis cells or in the spent culture supernatant fluid from M. catarrhalis. Use of the predicted MapA translocation domain in a fusion construct with the passenger domain from another predicted M. catarrhalis autotransporter confirmed the translocation ability of this MapA domain. Inactivation of the mapA gene in M. catarrhalis strain O35E reduced the acid phosphatase activity expressed by this organism, and this mutation could be complemented in trans with the wild-type mapA gene. Nucleotide sequence analysis of the mapA gene from six M. catarrhalis strains showed that this protein was highly conserved among strains of this pathogen. Site-directed mutagenesis of a critical histidine residue (H233A) in the predicted active site of the acid phosphatase domain in MapA eliminated acid phosphatase activity in the recombinant MapA protein. This is the first description of an autotransporter protein that expresses acid phosphatase activity. PMID:18065547

Contextualized analysis of a needs assessment using the Theoretical Domains Framework: a case example in endocrinology

PubMed Central

2014-01-01

Background The Theoretical Domains Framework (TDF) is a set of 14 domains of behavior change that provide a framework for the critical issues and factors influencing optimal knowledge translation. Considering that a previous study has identified optimal knowledge translation techniques for each TDF domain, it was hypothesized that the TDF could be used to contextualize and interpret findings from a behavioral and educational needs assessment. To illustrate this hypothesis, findings and recommendations drawn from a 2012 national behavioral and educational needs assessment conducted with healthcare providers who treat and manage Growth and Growth Hormone Disorders, will be discussed using the TDF. Methods This needs assessment utilized a mixed-methods research approach that included a combination of: [a] data sources (Endocrinologists (n:120), Pediatric Endocrinologists (n:53), Pediatricians (n:52)), [b] data collection methods (focus groups, interviews, online survey), [c] analysis methodologies (qualitative - analyzed through thematic analysis, quantitative - analyzed using frequencies, cross-tabulations, and gap analysis). Triangulation was used to generate trustworthy findings on the clinical practice gaps of endocrinologists, pediatric endocrinologists, and general pediatricians in their provision of care to adult patients with adult growth hormone deficiency or acromegaly, or children/teenagers with pediatric growth disorders. The identified gaps were then broken into key underlying determinants, categorized according to the TDF domains, and linked to optimal behavioral change techniques. Results The needs assessment identified 13 gaps, each with one or more underlying determinant(s). Overall, these determinants were mapped to 9 of the 14 TDF domains. The Beliefs about Consequences domain was identified as a contributing determinant to 7 of the 13 challenges. Five of the gaps could be related to the Skills domain, while three were linked to the Knowledge domain. Conclusions The TDF categorization of the needs assessment findings allowed recommendation of appropriate behavior change techniques for each underlying determinant, and facilitated communication and understanding of the identified issues to a broader audience. This approach provides a means for health education researchers to categorize gaps and challenges identified through educational needs assessments, and facilitates the application of these findings by educators and knowledge translators, by linking the gaps to recommended behavioral change techniques. PMID:25060235

Contextualized analysis of a needs assessment using the Theoretical Domains Framework: a case example in endocrinology.

PubMed

Lazure, Patrice; Bartel, Robert C; Biller, Beverly M K; Molitch, Mark E; Rosenthal, Stephen M; Ross, Judith L; Bernsten, Brock D; Hayes, Sean M

2014-07-24

The Theoretical Domains Framework (TDF) is a set of 14 domains of behavior change that provide a framework for the critical issues and factors influencing optimal knowledge translation. Considering that a previous study has identified optimal knowledge translation techniques for each TDF domain, it was hypothesized that the TDF could be used to contextualize and interpret findings from a behavioral and educational needs assessment. To illustrate this hypothesis, findings and recommendations drawn from a 2012 national behavioral and educational needs assessment conducted with healthcare providers who treat and manage Growth and Growth Hormone Disorders, will be discussed using the TDF. This needs assessment utilized a mixed-methods research approach that included a combination of: [a] data sources (Endocrinologists (n:120), Pediatric Endocrinologists (n:53), Pediatricians (n:52)), [b] data collection methods (focus groups, interviews, online survey), [c] analysis methodologies (qualitative - analyzed through thematic analysis, quantitative - analyzed using frequencies, cross-tabulations, and gap analysis). Triangulation was used to generate trustworthy findings on the clinical practice gaps of endocrinologists, pediatric endocrinologists, and general pediatricians in their provision of care to adult patients with adult growth hormone deficiency or acromegaly, or children/teenagers with pediatric growth disorders. The identified gaps were then broken into key underlying determinants, categorized according to the TDF domains, and linked to optimal behavioral change techniques. The needs assessment identified 13 gaps, each with one or more underlying determinant(s). Overall, these determinants were mapped to 9 of the 14 TDF domains. The Beliefs about Consequences domain was identified as a contributing determinant to 7 of the 13 challenges. Five of the gaps could be related to the Skills domain, while three were linked to the Knowledge domain. The TDF categorization of the needs assessment findings allowed recommendation of appropriate behavior change techniques for each underlying determinant, and facilitated communication and understanding of the identified issues to a broader audience. This approach provides a means for health education researchers to categorize gaps and challenges identified through educational needs assessments, and facilitates the application of these findings by educators and knowledge translators, by linking the gaps to recommended behavioral change techniques.

Space moving target detection using time domain feature

NASA Astrophysics Data System (ADS)

Wang, Min; Chen, Jin-yong; Gao, Feng; Zhao, Jin-yu

2018-01-01

The traditional space target detection methods mainly use the spatial characteristics of the star map to detect the targets, which can not make full use of the time domain information. This paper presents a new space moving target detection method based on time domain features. We firstly construct the time spectral data of star map, then analyze the time domain features of the main objects (target, stars and the background) in star maps, finally detect the moving targets using single pulse feature of the time domain signal. The real star map target detection experimental results show that the proposed method can effectively detect the trajectory of moving targets in the star map sequence, and the detection probability achieves 99% when the false alarm rate is about 8×10-5, which outperforms those of compared algorithms.

A knowledge representation approach using fuzzy cognitive maps for better navigation support in an adaptive learning system.

PubMed

Chrysafiadi, Konstantina; Virvou, Maria

2013-12-01

In this paper a knowledge representation approach of an adaptive and/or personalized tutoring system is presented. The domain knowledge should be represented in a more realistic way in order to allow the adaptive and/or personalized tutoring system to deliver the learning material to each individual learner dynamically taking into account her/his learning needs and her/his different learning pace. To succeed this, the domain knowledge representation has to depict the possible increase or decrease of the learner's knowledge. Considering that the domain concepts that constitute the learning material are not independent from each other, the knowledge representation approach has to allow the system to recognize either the domain concepts that are already partly or completely known for a learner, or the domain concepts that s/he has forgotten, taking into account the learner's knowledge level of the related concepts. In other words, the system should be informed about the knowledge dependencies that exist among the domain concepts of the learning material, as well as the strength on impact of each domain concept on others. Fuzzy Cognitive Maps (FCMs) seem to be an ideal way for representing graphically this kind of information. The suggested knowledge representation approach has been implemented in an e-learning adaptive system for teaching computer programming. The particular system was used by the students of a postgraduate program in the field of Informatics in the University of Piraeus and was compared with a corresponding system, in which the domain knowledge was represented using the most common used technique of network of concepts. The results of the evaluation were very encouraging.

Qualitative analysis and conceptual mapping of patient experiences in home health care.

PubMed

Lines, Lisa M; Anderson, Wayne L; Blackmon, Brian D; Pronier, Cristalle R; Allen, Rachael W; Kenyon, Anne E

2018-01-01

This study explored patient experiences in home health care through a literature review, focus groups, and interviews. Our goal was to develop a conceptual map of home health care patient experience domains. The conceptual map identifies technical and personal spheres of care, relating prior studies to new focus group and interview findings and identifying the most important domains of care. Study participants (n = 35) most frequently reported the most important domain as staff who are caring, supportive, patient, empathetic, respectful, and considerate (endorsed by 29% of participants). The conceptual map includes 114 discrete domains.

Terahertz near-field imaging of surface plasmon waves in graphene structures

DOE PAGES

Mitrofanov, O.; Yu, W.; Thompson, R. J.; ...

2015-09-08

In this study, we introduce a near-field scanning probe terahertz (THz) microscopy technique for probing surface plasmon waves on graphene. Based on THz time-domain spectroscopy method, this near-field imaging approach is well suited for studying the excitation and evolution of THz plasmon waves on graphene as well as for mapping of graphene properties at THz frequencies on the sub-wavelength scale.

Mapping subtrappean sediments and delineating structure with the aid of heliborne time domain electromagnetics: Case study from Kaladgi Basin, Karnataka

NASA Astrophysics Data System (ADS)

Sridhar, M.; Markandeyulu, A.; Chaturvedi, A. K.

2017-01-01

Mapping of subtrappean sediments is a complex geological problem attempted by many interpreters applying different geophysical techniques. Variations in thickness and resistivity of traps and underlying sediments, respectively, results in considerable uncertainty in the interpretation of geophysical data. It is proposed that the transient electromagnetic technique is an effective geophysical tool for delineation of the sub-trappean sediments, due to marked resistivity contrast between the Deccan trap, and underlying sediments and/or basement. The northern margin of the Kaladgi basin is covered under trap. A heliborne time domain electromagnetic survey was conducted to demarcate the basin extent and map the sub-trappean sediments. Conductivity depth transformations were used to map the interface between conductive trap and resistive 'basement'. Two resistivity contrast boundaries are picked: the first corresponds to the bottom of the shallow conductive unit interpreted as the base of the Deccan Volcanics and the second - picked at the base of a deeper subsurface conductive zone - is interpreted as the weathered paleo-surface of the crystalline basement. This second boundary can only be seen in areas where the volcanics are thin or absent, suggesting that the volcanics are masking the EM signal preventing deeper penetration. An interesting feature, which shows prominently in the EM data but less clearly imaged in the magnetic data, is observed in the vicinity of Mudhol. The surface geology interpreted from satellite imagery show Deccan trap cover around Mudhol. Modelling of TDEM data suggest the presence of synclinal basin structure. The depth of penetration of the heliborne TDEM data is estimated to be approximately 350 m for the study area. This suggests that heliborne TDEM could penetrate significant thicknesses of conductive Deccan trap cover to delineate structure below in the Bagalkot Group.

Automated mapping of clinical terms into SNOMED-CT. An application to codify procedures in pathology.

PubMed

Allones, J L; Martinez, D; Taboada, M

2014-10-01

Clinical terminologies are considered a key technology for capturing clinical data in a precise and standardized manner, which is critical to accurately exchange information among different applications, medical records and decision support systems. An important step to promote the real use of clinical terminologies, such as SNOMED-CT, is to facilitate the process of finding mappings between local terms of medical records and concepts of terminologies. In this paper, we propose a mapping tool to discover text-to-concept mappings in SNOMED-CT. Name-based techniques were combined with a query expansion system to generate alternative search terms, and with a strategy to analyze and take advantage of the semantic relationships of the SNOMED-CT concepts. The developed tool was evaluated and compared to the search services provided by two SNOMED-CT browsers. Our tool automatically mapped clinical terms from a Spanish glossary of procedures in pathology with 88.0% precision and 51.4% recall, providing a substantial improvement of recall (28% and 60%) over other publicly accessible mapping services. The improvements reached by the mapping tool are encouraging. Our results demonstrate the feasibility of accurately mapping clinical glossaries to SNOMED-CT concepts, by means a combination of structural, query expansion and named-based techniques. We have shown that SNOMED-CT is a great source of knowledge to infer synonyms for the medical domain. Results show that an automated query expansion system overcomes the challenge of vocabulary mismatch partially.

Seventh Graders' Academic Achievement, Creativity, and Ability to Construct a Cross-Domain Concept Map--A Brain Function Perspective

ERIC Educational Resources Information Center

Yeh, Yu-Chu

2004-01-01

This study proposes an interactive model of "cross-domain" concept mapping with an emphasis on brain functions, and it further investigates the relationships between academic achievement, creative thinking, and cross-domain concept mapping. Sixty-nine seventh graders participated in this study which employed two 50-minute instructional…

DOE Office of Scientific and Technical Information (OSTI.GOV)

Parlinski, K.; Hashi, Y.; Tsunekawa, S.

A model of lanthanum orthoniobate which possesses a ferroelastic tetragonal-monoclinic phase transition is proposed. It contains only one particle per unit cell, but it is constructed consistently with symmetry changes at the phase transition. The model parameters are chosen to reproduce the bare soft mode, degree of deformation of the tetragonal unit cell to monoclinic one, and the phase transition temperature. The ferroelastic system with free boundary conditions was simulated by the molecular dynamics technique, and the second order phase transition was reproduced. The studied annealing process shows formation of the stripe lenticular domain pattern, which has been interrupted bymore » appearance of a temporary band of perpendicularly oriented lenticular domains. The maps contain W{sup {prime}}-type domain walls whose orientations are fixed only by interplay of potential parameters and not by symmetry elements. The simulated domain pattern has the same features as those observed by transmission electron microscopy. {copyright} {ital 1997 Materials Research Society.}« less

Multilayer apparent magnetization mapping approach and its application in mineral exploration

NASA Astrophysics Data System (ADS)

Guo, L.; Meng, X.; Chen, Z.

2016-12-01

Apparent magnetization mapping is a technique to estimate magnetization distribution in the subsurface from the observed magnetic data. It has been applied for geologic mapping and mineral exploration for decades. Apparent magnetization mapping usually models the magnetic layer as a collection of vertical, juxtaposed prisms in both horizontal directions, whose top and bottom surfaces are assumed to be horizontal or variable-depth, and then inverts or deconvolves the magnetic anomalies in the space or frequency domain to determine the magnetization of each prism. The conventional mapping approaches usually assume that magnetic sources contain no remanent magnetization. However, such assumptions are not always valid in mineral exploration of metallic ores. In this case, the negligence of the remanence will result in large geologic deviation or the occurrence of negative magnetization. One alternate strategy is to transform the observed magnetic anomalies into some quantities that are insensitive or weakly sensitive to the remanence and then subsequently to perform inversion on these quantities, without needing any a priori information about remanent magnetization. Such kinds of quantities include the amplitude of the magnetic total field anomaly (AMA), and the normalized magnetic source strength (NSS). Here, we present a space-domain inversion approach for multilayer magnetization mapping based on the AMA for reducing effects of remanence. In the real world, magnetization usually varies vertically in the subsurface. If we use only one-layer model for mapping, the result is simply vertical superposition of different magnetization distributions. Hence, a multi-layer model for mapping would be a more realistic approach. We test the approach on the real data from a metallic deposit area in North China. The results demonstrated that our approach is feasible and produces considerable magnetization distribution from top layer to bottom layer in the subsurface.

Visualizing molecular polar order in tissues via electromechanical coupling

PubMed Central

Denning, Denise; Alilat, Sofiane; Habelitz, Stefan; Fertala, Andrzej; Rodriguez, Brian J.

2015-01-01

Electron microscopy (EM) and atomic force microscopy (AFM) techniques have long been used to characterize collagen fibril ordering and alignment in connective tissues. These techniques, however, are unable to map collagen fibril polarity, i.e., the polar orientation that is directed from the amine to the carboxyl termini. Using a voltage modulated AFM-based technique called piezoresponse force microscopy (PFM), we show it is possible to visualize both the alignment of collagen fibrils within a tissue and the polar orientation of the fibrils with minimal sample preparation. We demonstrate the technique on rat tail tendon and porcine eye tissues in ambient conditions. In each sample, fibrils are arranged into domains whereby neighboring domains exhibit opposite polarizations, which in some cases extend to the individual fibrillar level. Uniform polarity has not been observed in any of the tissues studied. Evidence of anti-parallel ordering of the amine to carboxyl polarity in bundles of fibrils or in individual fibrils is found in all tissues, which has relevance for understanding mechanical and biofunctional properties and the formation of connective tissues. The technique can be applied to any biological material containing piezoelectric biopolymers or polysaccharides. PMID:22985991

Linear and nonlinear frequency- and time-domain spectroscopy with multiple frequency combs.

PubMed

Bennett, Kochise; Rouxel, Jeremy R; Mukamel, Shaul

2017-09-07

Two techniques that employ equally spaced trains of optical pulses to map an optical high frequency into a low frequency modulation of the signal that can be detected in real time are compared. The development of phase-stable optical frequency combs has opened up new avenues to metrology and spectroscopy. The ability to generate a series of frequency spikes with precisely controlled separation permits a fast, highly accurate sampling of the material response. Recently, pairs of frequency combs with slightly different repetition rates have been utilized to down-convert material susceptibilities from the optical to microwave regime where they can be recorded in real time. We show how this one-dimensional dual comb technique can be extended to multiple dimensions by using several combs. We demonstrate how nonlinear susceptibilities can be quickly acquired using this technique. In a second class of techniques, sequences of ultrafast mode locked laser pulses are used to recover pathways of interactions contributing to nonlinear susceptibilities by using a photo-acoustic modulation varying along the sequences. We show that these techniques can be viewed as a time-domain analog of the multiple frequency comb scheme.

Page layout analysis and classification for complex scanned documents

NASA Astrophysics Data System (ADS)

Erkilinc, M. Sezer; Jaber, Mustafa; Saber, Eli; Bauer, Peter; Depalov, Dejan

2011-09-01

A framework for region/zone classification in color and gray-scale scanned documents is proposed in this paper. The algorithm includes modules for extracting text, photo, and strong edge/line regions. Firstly, a text detection module which is based on wavelet analysis and Run Length Encoding (RLE) technique is employed. Local and global energy maps in high frequency bands of the wavelet domain are generated and used as initial text maps. Further analysis using RLE yields a final text map. The second module is developed to detect image/photo and pictorial regions in the input document. A block-based classifier using basis vector projections is employed to identify photo candidate regions. Then, a final photo map is obtained by applying probabilistic model based on Markov random field (MRF) based maximum a posteriori (MAP) optimization with iterated conditional mode (ICM). The final module detects lines and strong edges using Hough transform and edge-linkages analysis, respectively. The text, photo, and strong edge/line maps are combined to generate a page layout classification of the scanned target document. Experimental results and objective evaluation show that the proposed technique has a very effective performance on variety of simple and complex scanned document types obtained from MediaTeam Oulu document database. The proposed page layout classifier can be used in systems for efficient document storage, content based document retrieval, optical character recognition, mobile phone imagery, and augmented reality.

A fusion algorithm for infrared and visible based on guided filtering and phase congruency in NSST domain

NASA Astrophysics Data System (ADS)

Liu, Zhanwen; Feng, Yan; Chen, Hang; Jiao, Licheng

2017-10-01

A novel and effective image fusion method is proposed for creating a highly informative and smooth surface of fused image through merging visible and infrared images. Firstly, a two-scale non-subsampled shearlet transform (NSST) is employed to decompose the visible and infrared images into detail layers and one base layer. Then, phase congruency is adopted to extract the saliency maps from the detail layers and a guided filtering is proposed to compute the filtering output of base layer and saliency maps. Next, a novel weighted average technique is used to make full use of scene consistency for fusion and obtaining coefficients map. Finally the fusion image was acquired by taking inverse NSST of the fused coefficients map. Experiments show that the proposed approach can achieve better performance than other methods in terms of subjective visual effect and objective assessment.

A novel data hiding scheme for block truncation coding compressed images using dynamic programming strategy

NASA Astrophysics Data System (ADS)

Chang, Ching-Chun; Liu, Yanjun; Nguyen, Son T.

2015-03-01

Data hiding is a technique that embeds information into digital cover data. This technique has been concentrated on the spatial uncompressed domain, and it is considered more challenging to perform in the compressed domain, i.e., vector quantization, JPEG, and block truncation coding (BTC). In this paper, we propose a new data hiding scheme for BTC-compressed images. In the proposed scheme, a dynamic programming strategy was used to search for the optimal solution of the bijective mapping function for LSB substitution. Then, according to the optimal solution, each mean value embeds three secret bits to obtain high hiding capacity with low distortion. The experimental results indicated that the proposed scheme obtained both higher hiding capacity and hiding efficiency than the other four existing schemes, while ensuring good visual quality of the stego-image. In addition, the proposed scheme achieved a low bit rate as original BTC algorithm.

3D FISH to analyse gene domain-specific chromatin re-modeling in human cancer cell lines.

PubMed

Kocanova, Silvia; Goiffon, Isabelle; Bystricky, Kerstin

2018-06-01

Fluorescence in situ hybridization (FISH) is a common technique used to label DNA and/or RNA for detection of a genomic region of interest. However, the technique can be challenging, in particular when applied to single genes in human cancer cells. Here, we provide a step-by-step protocol for analysis of short (35 kb-300 kb) genomic regions in three dimensions (3D). We discuss the experimental design and provide practical considerations for 3D imaging and data analysis to determine chromatin folding. We demonstrate that 3D FISH using BACs (Bacterial Artificial Chromosomes) or fosmids can provide detailed information of the architecture of gene domains. More specifically, we show that mapping of specific chromatin landscapes informs on changes associated with estrogen stimulated gene activity in human breast cancer cell lines. Copyright © 2018 Elsevier Inc. All rights reserved.

Signal Processing and Interpretation Using Multilevel Signal Abstractions.

DTIC Science & Technology

1986-06-01

mappings expressed in the Fourier domain. Pre- viously proposed causal analysis techniques for diagnosis are based on the analysis of intermediate data ...can be processed either as individual one-dimensional waveforms or as multichannel data 26 I P- - . . . ." " ." h9. for source detection and direction...microphone data . The signal processing for both spectral analysis of microphone signals and direc- * tion determination of acoustic sources involves

Performance evaluation of digital phase-locked loops for advanced deep space transponders

NASA Technical Reports Server (NTRS)

Nguyen, T. M.; Hinedi, S. M.; Yeh, H.-G.; Kyriacou, C.

1994-01-01

The performances of the digital phase-locked loops (DPLL's) for the advanced deep-space transponders (ADT's) are investigated. DPLL's considered in this article are derived from the analog phase-locked loop, which is currently employed by the NASA standard deep space transponder, using S-domain to Z-domain mapping techniques. Three mappings are used to develop digital approximations of the standard deep space analog phase-locked loop, namely the bilinear transformation (BT), impulse invariant transformation (IIT), and step invariant transformation (SIT) techniques. The performance in terms of the closed loop phase and magnitude responses, carrier tracking jitter, and response of the loop to the phase offset (the difference between in incoming phase and reference phase) is evaluated for each digital approximation. Theoretical results of the carrier tracking jitter for command-on and command-off cases are then validated by computer simulation. Both theoretical and computer simulation results show that at high sampling frequency, the DPLL's approximated by all three transformations have the same tracking jitter. However, at low sampling frequency, the digital approximation using BT outperforms the others. The minimum sampling frequency for adequate tracking performance is determined for each digital approximation of the analog loop. In addition, computer simulation shows that the DPLL developed by BT provides faster response to the phase offset than IIT and SIT.

Globally optimal superconducting magnets part I: minimum stored energy (MSE) current density map.

PubMed

Tieng, Quang M; Vegh, Viktor; Brereton, Ian M

2009-01-01

An optimal current density map is crucial in magnet design to provide the initial values within search spaces in an optimization process for determining the final coil arrangement of the magnet. A strategy for obtaining globally optimal current density maps for the purpose of designing magnets with coaxial cylindrical coils in which the stored energy is minimized within a constrained domain is outlined. The current density maps obtained utilising the proposed method suggests that peak current densities occur around the perimeter of the magnet domain, where the adjacent peaks have alternating current directions for the most compact designs. As the dimensions of the domain are increased, the current density maps yield traditional magnet designs of positive current alone. These unique current density maps are obtained by minimizing the stored magnetic energy cost function and therefore suggest magnet coil designs of minimal system energy. Current density maps are provided for a number of different domain arrangements to illustrate the flexibility of the method and the quality of the achievable designs.

Geometrical and topological issues in octree based automatic meshing

NASA Technical Reports Server (NTRS)

Saxena, Mukul; Perucchio, Renato

1987-01-01

Finite element meshes derived automatically from solid models through recursive spatial subdivision schemes (octrees) can be made to inherit the hierarchical structure and the spatial addressability intrinsic to the underlying grid. These two properties, together with the geometric regularity that can also be built into the mesh, make octree based meshes ideally suited for efficient analysis and self-adaptive remeshing and reanalysis. The element decomposition of the octal cells that intersect the boundary of the domain is discussed. The problem, central to octree based meshing, is solved by combining template mapping and element extraction into a procedure that utilizes both constructive solid geometry and boundary representation techniques. Boundary cells that are not intersected by the edge of the domain boundary are easily mapped to predefined element topology. Cells containing edges (and vertices) are first transformed into a planar polyhedron and then triangulated via element extractor. The modeling environments required for the derivation of planar polyhedra and for element extraction are analyzed.

Octree based automatic meshing from CSG models

NASA Technical Reports Server (NTRS)

Perucchio, Renato

1987-01-01

Finite element meshes derived automatically from solid models through recursive spatial subdivision schemes (octrees) can be made to inherit the hierarchical structure and the spatial addressability intrinsic to the underlying grid. These two properties, together with the geometric regularity that can also be built into the mesh, make octree based meshes ideally suited for efficient analysis and self-adaptive remeshing and reanalysis. The element decomposition of the octal cells that intersect the boundary of the domain is emphasized. The problem, central to octree based meshing, is solved by combining template mapping and element extraction into a procedure that utilizes both constructive solid geometry and boundary respresentation techniques. Boundary cells that are not intersected by the edge of the domain boundary are easily mapped to predefined element topology. Cells containing edges (and vertices) are first transformed into a planar polyhedron and then triangulated via element extractors. The modeling environments required for the derivation of planar polyhedra and for element extraction are analyzed.

Domain repertoires as a tool to derive protein recognition rules.

PubMed

Zucconi, A; Panni, S; Paoluzi, S; Castagnoli, L; Dente, L; Cesareni, G

2000-08-25

Several approaches, some of which are described in this issue, have been proposed to assemble a complete protein interaction map. These are often based on high throughput methods that explore the ability of each gene product to bind any other element of the proteome of the organism. Here we propose that a large number of interactions can be inferred by revealing the rules underlying recognition specificity of a small number (a few hundreds) of families of protein recognition modules. This can be achieved through the construction and characterization of domain repertoires. A domain repertoire is assembled in a combinatorial fashion by allowing each amino acid position in the binding site of a given protein recognition domain to vary to include all the residues allowed at that position in the domain family. The repertoire is then searched by phage display techniques with any target of interest and from the primary structure of the binding site of the selected domains one derives rules that are used to infer the formation of complexes between natural proteins in the cell.

Mapping small molecule binding data to structural domains

PubMed Central

2012-01-01

Background Large-scale bioactivity/SAR Open Data has recently become available, and this has allowed new analyses and approaches to be developed to help address the productivity and translational gaps of current drug discovery. One of the current limitations of these data is the relative sparsity of reported interactions per protein target, and complexities in establishing clear relationships between bioactivity and targets using bioinformatics tools. We detail in this paper the indexing of targets by the structural domains that bind (or are likely to bind) the ligand within a full-length protein. Specifically, we present a simple heuristic to map small molecule binding to Pfam domains. This profiling can be applied to all proteins within a genome to give some indications of the potential pharmacological modulation and regulation of all proteins. Results In this implementation of our heuristic, ligand binding to protein targets from the ChEMBL database was mapped to structural domains as defined by profiles contained within the Pfam-A database. Our mapping suggests that the majority of assay targets within the current version of the ChEMBL database bind ligands through a small number of highly prevalent domains, and conversely the majority of Pfam domains sampled by our data play no currently established role in ligand binding. Validation studies, carried out firstly against Uniprot entries with expert binding-site annotation and secondly against entries in the wwPDB repository of crystallographic protein structures, demonstrate that our simple heuristic maps ligand binding to the correct domain in about 90 percent of all assessed cases. Using the mappings obtained with our heuristic, we have assembled ligand sets associated with each Pfam domain. Conclusions Small molecule binding has been mapped to Pfam-A domains of protein targets in the ChEMBL bioactivity database. The result of this mapping is an enriched annotation of small molecule bioactivity data and a grouping of activity classes following the Pfam-A specifications of protein domains. This is valuable for data-focused approaches in drug discovery, for example when extrapolating potential targets of a small molecule with known activity against one or few targets, or in the assessment of a potential target for drug discovery or screening studies. PMID:23282026

Ordered mapping of 3 alphoid DNA subsets on human chromosome 22

DOE Office of Scientific and Technical Information (OSTI.GOV)

Antonacci, R.; Baldini, A.; Archidiacono, N.

1994-09-01

Alpha satellite DNA consists of tandemly repeated monomers of 171 bp clustered in the centromeric region of primate chromosomes. Sequence divergence between subsets located in different human chromosomes is usually high enough to ensure chromosome-specific hybridization. Alphoid probes specific for almost every human chromosome have been reported. A single chromosome can carry different subsets of alphoid DNA and some alphoid subsets can be shared by different chromosomes. We report the physical order of three alphoid DNA subsets on human chromosome 22 determined by a combination of low and high resolution cytological mapping methods. Results visually demonstrate the presence of threemore » distinct alphoid DNA domains at the centromeric region of chromosome 22. We have measured the interphase distances between the three probes in three-color FISH experiments. Statistical analysis of the results indicated the order of the subsets. Two color experiments on prometaphase chromosomes established the order of the three domains relative to the arms of chromosome 22 and confirmed the results obtained using interphase mapping. This demonstrates the applicability of interphase mapping for alpha satellite DNA orderering. However, in our experiments, interphase mapping did not provide any information about the relationship between extremities of the repeat arrays. This information was gained from extended chromatin hybridization. The extremities of two of the repeat arrays were seen to be almost overlapping whereas the third repeat array was clearly separated from the other two. Our data show the value of extended chromatin hybridization as a complement of other cytological techniques for high resolution mapping of repetitive DNA sequences.« less

Visualization of system dynamics using phasegrams

PubMed Central

Herbst, Christian T.; Herzel, Hanspeter; Švec, Jan G.; Wyman, Megan T.; Fitch, W. Tecumseh

2013-01-01

A new tool for visualization and analysis of system dynamics is introduced: the phasegram. Its application is illustrated with both classical nonlinear systems (logistic map and Lorenz system) and with biological voice signals. Phasegrams combine the advantages of sliding-window analysis (such as the spectrogram) with well-established visualization techniques from the domain of nonlinear dynamics. In a phasegram, time is mapped onto the x-axis, and various vibratory regimes, such as periodic oscillation, subharmonics or chaos, are identified within the generated graph by the number and stability of horizontal lines. A phasegram can be interpreted as a bifurcation diagram in time. In contrast to other analysis techniques, it can be automatically constructed from time-series data alone: no additional system parameter needs to be known. Phasegrams show great potential for signal classification and can act as the quantitative basis for further analysis of oscillating systems in many scientific fields, such as physics (particularly acoustics), biology or medicine. PMID:23697715

Strain distribution across a partially molten middle crust: Insights from the AMS mapping of the Carlos Chagas Anatexite, Araçuaí belt (East Brazil)

NASA Astrophysics Data System (ADS)

Cavalcante, Geane C. G.; Egydio-Silva, Marcos; Vauchez, Alain; Camps, Pierre; Oliveira, Eurídice

2013-10-01

The easternmost part of the Neoproterozoic Araçuaí belt comprises an anatectic domain that involves anatexites (the Carlos Chagas unit), leucogranites and migmatitic granulites that display a well-developed fabric. Microstructural observations support that the deformation occurred in the magmatic to submagmatic state. Structural mapping integrating field and anisotropy of magnetic susceptibility (AMS) revealed a complex, 3D structure. The northern domain displays gently dipping foliations bearing a NW-trending lineation, southward, the lineation trend progressively rotates to EW then SW and the foliation is gently folded. The eastern domain displays E-W and NE-SW trending foliations with moderate to steeply dips bearing a dominantly NS trending lineation. Magnetic mineralogy investigation suggests biotite as the main carrier of the magnetic susceptibility in the anatexites and ferromagnetic minerals in the granulites. Crystallographic preferred orientation (CPO) measurements using the electron backscatter diffraction (EBSD) technique suggest that the magnetic fabric comes from the crystalline anisotropy of biotite and feldspar grains, especially. The delineation of several structural domains with contrasted flow fabric suggests a 3D flow field involving westward thrusting orthogonal to the belt, northwestward orogen-oblique escape tectonics and NS orogen-parallel flow. This complex deformation pattern may be due to interplay of collision-driven and gravity-driven deformations.

PPDMs-a resource for mapping small molecule bioactivities from ChEMBL to Pfam-A protein domains.

PubMed

Kruger, Felix A; Gaulton, Anna; Nowotka, Michal; Overington, John P

2015-03-01

PPDMs is a resource that maps small molecule bioactivities to protein domains from the Pfam-A collection of protein families. Small molecule bioactivities mapped to protein domains add important precision to approaches that use protein sequence searches alignments to assist applications in computational drug discovery and systems and chemical biology. We have previously proposed a mapping heuristic for a subset of bioactivities stored in ChEMBL with the Pfam-A domain most likely to mediate small molecule binding. We have since refined this mapping using a manual procedure. Here, we present a resource that provides up-to-date mappings and the possibility to review assigned mappings as well as to participate in their assignment and curation. We also describe how mappings provided through the PPDMs resource are made accessible through the main schema of the ChEMBL database. The PPDMs resource and curation interface is available at https://www.ebi.ac.uk/chembl/research/ppdms/pfam_maps. The source-code for PPDMs is available under the Apache license at https://github.com/chembl/pfam_maps. Source code is available at https://github.com/chembl/pfam_map_loader to demonstrate the integration process with the main schema of ChEMBL. © The Author 2014. Published by Oxford University Press.

Beethoven's Last Piano Sonata and Those Who Follow Crocodiles: Cross-Domain Mappings of Auditory Pitch in a Musical Context

ERIC Educational Resources Information Center

Eitan, Zohar; Timmers, Renee

2010-01-01

Though auditory pitch is customarily mapped in Western cultures onto spatial verticality (high-low), both anthropological reports and cognitive studies suggest that pitch may be mapped onto a wide variety of other domains. We collected a total number of 35 pitch mappings and investigated in four experiments how these mappings are used and…

Elucidation of the internal physical and chemical microstructure of pharmaceutical granules using X-ray micro-computed tomography, Raman microscopy and infrared spectroscopy.

PubMed

Crean, Barry; Parker, Andrew; Roux, Delphine Le; Perkins, Mark; Luk, Shen Y; Banks, Simon R; Melia, Colin D; Roberts, Clive J

2010-11-01

X-ray micro-computed tomography (XMCT) was used in conjunction with confocal Raman mapping to measure the intra-granular pore size, binder volumes and to provide spatial and chemical maps of internal granular components in α-lactose monohydrate granules formulated with different molecular weights of polyvinyl pyrrolidone (PVP). Infrared spectroscopy was used to understand the molecular association of binder domains. Granules were prepared by high-shear aqueous granulation from α-lactose monohydrate and PVP K29/32 or K90. XMCT was used to visualise the granule microstructure, intra-granular binder distribution and measure intra-granular porosity, which was subsequently related to intrusion porosimetry measurements. Confocal Raman microscopy and infrared microscopy were employed to investigate the distribution of components within the granule and explore the nature of binder substrate interactions. XMCT data sets of internal granule microstructure provided values of residual porosity in the lactose:PVP K29/32 and lactose:PVP K90 granules of 32.41 ± 4.60% and 22.40 ± 0.03%, respectively. The binder volumes of the lactose:PVP K29/32 and lactose:PVP K90 granules were 2.98 ± 0.10% and 3.38 ± 0.07%, respectively, and were attributed to PVP-rich binder domains within the granule. Confocal Raman microscopy revealed anisotropic domains of PVP between 2 μm and 20 μm in size surrounded by larger particles of lactose, in both granule types. Raman data showed that PVP domains contained various amounts of lactose, whilst IR microscopy determined that the PVP was molecularly associated with lactose, rather than residual water. The work shows that XMCT can be applied to investigate granular microstructure and resolve the porosity and the excipient and binder volumes. Combining this technique with vibrational techniques provides further structural information and aids the interpretations of the XMCT images. When used complementarily, these techniques highlighted that porosity and binder volume were the most significant microstructural differences between the α-lactose monohydrate granules formulated with the different grades of PVP. Copyright © 2010 Elsevier B.V. All rights reserved.

Semantic characteristics of NLP-extracted concepts in clinical notes vs. biomedical literature.

PubMed

Wu, Stephen; Liu, Hongfang

2011-01-01

Natural language processing (NLP) has become crucial in unlocking information stored in free text, from both clinical notes and biomedical literature. Clinical notes convey clinical information related to individual patient health care, while biomedical literature communicates scientific findings. This work focuses on semantic characterization of texts at an enterprise scale, comparing and contrasting the two domains and their NLP approaches. We analyzed the empirical distributional characteristics of NLP-discovered named entities in Mayo Clinic clinical notes from 2001-2010, and in the 2011 MetaMapped Medline Baseline. We give qualitative and quantitative measures of domain similarity and point to the feasibility of transferring resources and techniques. An important by-product for this study is the development of a weighted ontology for each domain, which gives distributional semantic information that may be used to improve NLP applications.

BioPortal: An Open-Source Community-Based Ontology Repository

NASA Astrophysics Data System (ADS)

Noy, N.; NCBO Team

2011-12-01

Advances in computing power and new computational techniques have changed the way researchers approach science. In many fields, one of the most fruitful approaches has been to use semantically aware software to break down the barriers among disparate domains, systems, data sources, and technologies. Such software facilitates data aggregation, improves search, and ultimately allows the detection of new associations that were previously not detectable. Achieving these analyses requires software systems that take advantage of the semantics and that can intelligently negotiate domains and knowledge sources, identifying commonality across systems that use different and conflicting vocabularies, while understanding apparent differences that may be concealed by the use of superficially similar terms. An ontology, a semantically rich vocabulary for a domain of interest, is the cornerstone of software for bridging systems, domains, and resources. However, as ontologies become the foundation of all semantic technologies in e-science, we must develop an infrastructure for sharing ontologies, finding and evaluating them, integrating and mapping among them, and using ontologies in applications that help scientists process their data. BioPortal [1] is an open-source on-line community-based ontology repository that has been used as a critical component of semantic infrastructure in several domains, including biomedicine and bio-geochemical data. BioPortal, uses the social approaches in the Web 2.0 style to bring structure and order to the collection of biomedical ontologies. It enables users to provide and discuss a wide array of knowledge components, from submitting the ontologies themselves, to commenting on and discussing classes in the ontologies, to reviewing ontologies in the context of their own ontology-based projects, to creating mappings between overlapping ontologies and discussing and critiquing the mappings. Critically, it provides web-service access to all its content, enabling its integration in semantically enriched applications. [1] Noy, N.F., Shah, N.H., et al., BioPortal: ontologies and integrated data resources at the click of a mouse. Nucleic Acids Res, 2009. 37(Web Server issue): p. W170-3.

Beethoven's last piano sonata and those who follow crocodiles: cross-domain mappings of auditory pitch in a musical context.

PubMed

Eitan, Zohar; Timmers, Renee

2010-03-01

Though auditory pitch is customarily mapped in Western cultures onto spatial verticality (high-low), both anthropological reports and cognitive studies suggest that pitch may be mapped onto a wide variety of other domains. We collected a total number of 35 pitch mappings and investigated in four experiments how these mappings are used and structured. In particular, we inquired (1) how Western subjects apply Western and non-Western metaphors to "high" and "low" pitches, (2) whether mappings applied in an abstract conceptual task are similarly applied by listeners to actual music, (3) how mappings of spatial height relate to these pitch mappings, and (4) how mappings of "high" and "low" pitch associate with other dimensions, in particular quantity, size, intensity and valence. The results show strong agreement among Western participants in applying familiar and unfamiliar metaphors for pitch, in both an abstract, conceptual task (Exp. 1) and in a music listening task (Exp. 2), indicating that diverse cross-domain mappings for pitch exist latently besides the common verticality metaphor. Furthermore, limited overlap between mappings of spatial height and pitch height was found, suggesting that, the ubiquity of the verticality metaphor in Western usage notwithstanding, cross-domain pitch mappings are largely independent of that metaphor, and seem to be based upon other underlying dimensions. Part of the discrepancy between spatial height and pitch height is that, for pitch, "up" is not necessarily "more," nor is it necessarily "good." High pitch is only "more" for height, intensity and brightness. It is "less" for mass, size and quantity. We discuss implications of these findings for music and speech prosody, and their relevance to notions of embodied cognition and of cross-domain magnitude representation. Copyright 2009 Elsevier B.V. All rights reserved.

Cerebral autoregulation in the preterm newborn using near-infrared spectroscopy: a comparison of time-domain and frequency-domain analyses

NASA Astrophysics Data System (ADS)

Eriksen, Vibeke R.; Hahn, Gitte H.; Greisen, Gorm

2015-03-01

The aim was to compare two conventional methods used to describe cerebral autoregulation (CA): frequency-domain analysis and time-domain analysis. We measured cerebral oxygenation (as a surrogate for cerebral blood flow) and mean arterial blood pressure (MAP) in 60 preterm infants. In the frequency domain, outcome variables were coherence and gain, whereas the cerebral oximetry index (COx) and the regression coefficient were the outcome variables in the time domain. Correlation between coherence and COx was poor. The disagreement between the two methods was due to the MAP and cerebral oxygenation signals being in counterphase in three cases. High gain and high coherence may arise spuriously when cerebral oxygenation decreases as MAP increases; hence, time-domain analysis appears to be a more robust-and simpler-method to describe CA.

Towards Inferring Protein Interactions: Challenges and Solutions

NASA Astrophysics Data System (ADS)

Zhang, Ya; Zha, Hongyuan; Chu, Chao-Hsien; Ji, Xiang

2006-12-01

Discovering interacting proteins has been an essential part of functional genomics. However, existing experimental techniques only uncover a small portion of any interactome. Furthermore, these data often have a very high false rate. By conceptualizing the interactions at domain level, we provide a more abstract representation of interactome, which also facilitates the discovery of unobserved protein-protein interactions. Although several domain-based approaches have been proposed to predict protein-protein interactions, they usually assume that domain interactions are independent on each other for the convenience of computational modeling. A new framework to predict protein interactions is proposed in this paper, where no assumption is made about domain interactions. Protein interactions may be the result of multiple domain interactions which are dependent on each other. A conjunctive norm form representation is used to capture the relationships between protein interactions and domain interactions. The problem of interaction inference is then modeled as a constraint satisfiability problem and solved via linear programing. Experimental results on a combined yeast data set have demonstrated the robustness and the accuracy of the proposed algorithm. Moreover, we also map some predicted interacting domains to three-dimensional structures of protein complexes to show the validity of our predictions.

Linear time relational prototype based learning.

PubMed

Gisbrecht, Andrej; Mokbel, Bassam; Schleif, Frank-Michael; Zhu, Xibin; Hammer, Barbara

2012-10-01

Prototype based learning offers an intuitive interface to inspect large quantities of electronic data in supervised or unsupervised settings. Recently, many techniques have been extended to data described by general dissimilarities rather than Euclidean vectors, so-called relational data settings. Unlike the Euclidean counterparts, the techniques have quadratic time complexity due to the underlying quadratic dissimilarity matrix. Thus, they are infeasible already for medium sized data sets. The contribution of this article is twofold: On the one hand we propose a novel supervised prototype based classification technique for dissimilarity data based on popular learning vector quantization (LVQ), on the other hand we transfer a linear time approximation technique, the Nyström approximation, to this algorithm and an unsupervised counterpart, the relational generative topographic mapping (GTM). This way, linear time and space methods result. We evaluate the techniques on three examples from the biomedical domain.

A vector scanning processing technique for pulsed laser velocimetry

NASA Technical Reports Server (NTRS)

Wernet, Mark P.; Edwards, Robert V.

1989-01-01

Pulsed-laser-sheet velocimetry yields two-dimensional velocity vectors across an extended planar region of a flow. Current processing techniques offer high-precision (1-percent) velocity estimates, but can require hours of processing time on specialized array processors. Sometimes, however, a less accurate (about 5 percent) data-reduction technique which also gives unambiguous velocity vector information is acceptable. Here, a direct space-domain processing technique is described and shown to be far superior to previous methods in achieving these objectives. It uses a novel data coding and reduction technique and has no 180-deg directional ambiguity. A complex convection vortex flow was recorded and completely processed in under 2 min on an 80386-based PC, producing a two-dimensional velocity-vector map of the flowfield. Pulsed-laser velocimetry data can thus be reduced quickly and reasonably accurately, without specialized array processing hardware.

Management of Dynamic Biomedical Terminologies: Current Status and Future Challenges

PubMed Central

Dos Reis, J. C.; Pruski, C.

2015-01-01

Summary Objectives Controlled terminologies and their dependent artefacts provide a consensual understanding of a domain while reducing ambiguities and enabling reasoning. However, the evolution of a domain’s knowledge directly impacts these terminologies and generates inconsistencies in the underlying biomedical information systems. In this article, we review existing work addressing the dynamic aspect of terminologies as well as their effects on mappings and semantic annotations. Methods We investigate approaches related to the identification, characterization and propagation of changes in terminologies, mappings and semantic annotations including techniques to update their content. Results and conclusion Based on the explored issues and existing methods, we outline open research challenges requiring investigation in the near future. PMID:26293859

Local coexistence of VO 2 phases revealed by deep data analysis

DOE PAGES

Strelcov, Evgheni; Ievlev, Anton; Tselev, Alexander; ...

2016-07-07

We report a synergistic approach of micro-Raman spectroscopic mapping and deep data analysis to study the distribution of crystallographic phases and ferroelastic domains in a defected Al-doped VO 2 microcrystal. Bayesian linear unmixing revealed an uneven distribution of the T phase, which is stabilized by the surface defects and uneven local doping that went undetectable by other classical analysis techniques such as PCA and SIMPLISMA. This work demonstrates the impact of information recovery via statistical analysis and full mapping in spectroscopic studies of vanadium dioxide systems, which is commonly substituted by averaging or single point-probing approaches, both of which suffermore » from information misinterpretation due to low resolving power.« less

DIMA 3.0: Domain Interaction Map.

PubMed

Luo, Qibin; Pagel, Philipp; Vilne, Baiba; Frishman, Dmitrij

2011-01-01

Domain Interaction MAp (DIMA, available at http://webclu.bio.wzw.tum.de/dima) is a database of predicted and known interactions between protein domains. It integrates 5807 structurally known interactions imported from the iPfam and 3did databases and 46,900 domain interactions predicted by four computational methods: domain phylogenetic profiling, domain pair exclusion algorithm correlated mutations and domain interaction prediction in a discriminative way. Additionally predictions are filtered to exclude those domain pairs that are reported as non-interacting by the Negatome database. The DIMA Web site allows to calculate domain interaction networks either for a domain of interest or for entire organisms, and to explore them interactively using the Flash-based Cytoscape Web software.

Compressed-domain video indexing techniques using DCT and motion vector information in MPEG video

NASA Astrophysics Data System (ADS)

Kobla, Vikrant; Doermann, David S.; Lin, King-Ip; Faloutsos, Christos

1997-01-01

Development of various multimedia applications hinges on the availability of fast and efficient storage, browsing, indexing, and retrieval techniques. Given that video is typically stored efficiently in a compressed format, if we can analyze the compressed representation directly, we can avoid the costly overhead of decompressing and operating at the pixel level. Compressed domain parsing of video has been presented in earlier work where a video clip is divided into shots, subshots, and scenes. In this paper, we describe key frame selection, feature extraction, and indexing and retrieval techniques that are directly applicable to MPEG compressed video. We develop a frame-type independent representation of the various types of frames present in an MPEG video in which al frames can be considered equivalent. Features are derived from the available DCT, macroblock, and motion vector information and mapped to a low-dimensional space where they can be accessed with standard database techniques. The spatial information is used as primary index while the temporal information is used to enhance the robustness of the system during the retrieval process. The techniques presented enable fast archiving, indexing, and retrieval of video. Our operational prototype typically takes a fraction of a second to retrieve similar video scenes from our database, with over 95% success.

Domain Visualization Using VxInsight[R] for Science and Technology Management.

ERIC Educational Resources Information Center

Boyack, Kevin W.; Wylie, Brian N.; Davidson, George S.

2002-01-01

Presents the application of a knowledge visualization tool, VxInsight[R], to enable domain analysis for science and technology management. Uses data mining from sources of bibliographic information to define subsets of relevant information and discusses citation mapping, text mapping, and journal mapping. (Author/LRW)

Crystal structure of the catalytic domain of PigE: a transaminase involved in the biosynthesis of 2-methyl-3-n-amyl-pyrrole (MAP) from Serratia sp. FS14.

PubMed

Lou, Xiangdi; Ran, Tingting; Han, Ning; Gao, Yanyan; He, Jianhua; Tang, Lin; Xu, Dongqing; Wang, Weiwu

2014-04-25

Prodigiosin, a tripyrrole red pigment synthesized by Serratia and some other microbes through a bifurcated biosynthesis pathway, MBC (4-methoxy-2,2'-bipyrrole-5-carbaldehyde) and MAP (2-methyl-3-n-amyl-pyrrole) are synthesized separately and then condensed by PigC to form prodigiosin. MAP is synthesized sequentially by PigD, PigE and PigB. PigE catalyzes the transamination of an amino group to the aldehyde group of 3-acetyloctanal, resulting in an aminoketone, which spontaneously cyclizes to form H2MAP. Here we report the crystal structure of the catalytic domain of PigE which involved in the biosynthesis of prodigiosin precursor MAP for the first time to a resolution of 2.3Å with a homodimer in the asymmetric unit. The monomer of PigE catalytic domain is composed of three domains with PLP as cofactor: a small N-terminal domain connecting the catalytic domain with the front part of PigE, a large PLP-binding domain and a C-terminal domain. The residues from both monomers build the PLP binding site at the interface of the dimer which resembles the other PLP-dependent enzymes. Structural comparison of PigE with Thermus thermophilus AcOAT showed a higher hydrophobic and smaller active site of PigE, these differences may be the reason for substrate specificity. Copyright © 2014 Elsevier Inc. All rights reserved.

Optimal mapping of irregular finite element domains to parallel processors

NASA Technical Reports Server (NTRS)

Flower, J.; Otto, S.; Salama, M.

1987-01-01

Mapping the solution domain of n-finite elements into N-subdomains that may be processed in parallel by N-processors is an optimal one if the subdomain decomposition results in a well-balanced workload distribution among the processors. The problem is discussed in the context of irregular finite element domains as an important aspect of the efficient utilization of the capabilities of emerging multiprocessor computers. Finding the optimal mapping is an intractable combinatorial optimization problem, for which a satisfactory approximate solution is obtained here by analogy to a method used in statistical mechanics for simulating the annealing process in solids. The simulated annealing analogy and algorithm are described, and numerical results are given for mapping an irregular two-dimensional finite element domain containing a singularity onto the Hypercube computer.

Cross-sectional mapping for refined beam elements with applications to shell-like structures

NASA Astrophysics Data System (ADS)

Pagani, A.; de Miguel, A. G.; Carrera, E.

2017-06-01

This paper discusses the use of higher-order mapping functions for enhancing the physical representation of refined beam theories. Based on the Carrera unified formulation (CUF), advanced one-dimensional models are formulated by expressing the displacement field as a generic expansion of the generalized unknowns. According to CUF, a novel physically/geometrically consistent model is devised by employing Legendre-like polynomial sets to approximate the generalized unknowns at the cross-sectional level, whereas a local mapping technique based on the blending functions method is used to describe the exact physical boundaries of the cross-section domain. Classical and innovative finite element methods, including hierarchical p-elements and locking-free integration schemes, are utilized to solve the governing equations of the unified beam theory. Several numerical applications accounting for small displacements/rotations and strains are discussed, including beam structures with cross-sectional curved edges, cylindrical shells, and thin-walled aeronautical wing structures with reinforcements. The results from the proposed methodology are widely assessed by comparisons with solutions from the literature and commercial finite element software tools. The attention is focussed on the high computational efficiency and the marked capabilities of the present beam model, which can deal with a broad spectrum of structural problems with unveiled accuracy in terms of geometrical representation of the domain boundaries.

An Image Morphing Technique Based on Optimal Mass Preserving Mapping

DTIC Science & Technology

2007-06-01

Yan Yang, Steven Haker , and Allen Tannenbaum Abstract—Image morphing, or image interpolation in the time domain, deals with the metamorphosis of one...of Technology, Atlanta, GA 30332 USA (e-mail: zlzl@ece.gatech.edu; zhulei1976@hotmail.com; yan.yang@gatech.edu; tannenba@ece.gatech.edu). S. Haker is...with the Surgical Planning Laboratory, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115 USA (e-mail: haker @bwh.harvard.edu

Diffuse shear wave imaging: toward passive elastography using low-frame rate spectral-domain optical coherence tomography

NASA Astrophysics Data System (ADS)

Nguyen, Thu-Mai; Zorgani, Ali; Lescanne, Maxime; Boccara, Claude; Fink, Mathias; Catheline, Stefan

2016-12-01

Optical coherence tomography (OCT) can map the stiffness of biological tissue by imaging mechanical perturbations (shear waves) propagating in the tissue. Most shear wave elastography (SWE) techniques rely on active shear sources to generate controlled displacements that are tracked at ultrafast imaging rates. Here, we propose a noise-correlation approach to retrieve stiffness information from the imaging of diffuse displacement fields using low-frame rate spectral-domain OCT. We demonstrated the method on tissue-mimicking phantoms and validated the results by comparison with classic ultrafast SWE. Then we investigated the in vivo feasibility on the eye of an anesthetized rat by applying noise correlation to naturally occurring displacements. The results suggest a great potential for passive elastography based on the detection of natural pulsatile motions using conventional spectral-domain OCT systems. This would facilitate the transfer of OCT-elastography to clinical practice, in particular, in ophthalmology or dermatology.

Diffuse shear wave imaging: toward passive elastography using low-frame rate spectral-domain optical coherence tomography.

PubMed

Nguyen, Thu-Mai; Zorgani, Ali; Lescanne, Maxime; Boccara, Claude; Fink, Mathias; Catheline, Stefan

2016-12-01

Optical coherence tomography (OCT) can map the stiffness of biological tissue by imaging mechanical perturbations (shear waves) propagating in the tissue. Most shear wave elastography (SWE) techniques rely on active shear sources to generate controlled displacements that are tracked at ultrafast imaging rates. Here, we propose a noise-correlation approach to retrieve stiffness information from the imaging of diffuse displacement fields using low-frame rate spectral-domain OCT. We demonstrated the method on tissue-mimicking phantoms and validated the results by comparison with classic ultrafast SWE. Then we investigated the in vivo feasibility on the eye of an anesthetized rat by applying noise correlation to naturally occurring displacements. The results suggest a great potential for passive elastography based on the detection of natural pulsatile motions using conventional spectral-domain OCT systems. This would facilitate the transfer of OCT-elastography to clinical practice, in particular, in ophthalmology or dermatology.

An intelligent user interface for browsing satellite data catalogs

NASA Technical Reports Server (NTRS)

Cromp, Robert F.; Crook, Sharon

1989-01-01

A large scale domain-independent spatial data management expert system that serves as a front-end to databases containing spatial data is described. This system is unique for two reasons. First, it uses spatial search techniques to generate a list of all the primary keys that fall within a user's spatial constraints prior to invoking the database management system, thus substantially decreasing the amount of time required to answer a user's query. Second, a domain-independent query expert system uses a domain-specific rule base to preprocess the user's English query, effectively mapping a broad class of queries into a smaller subset that can be handled by a commercial natural language processing system. The methods used by the spatial search module and the query expert system are explained, and the system architecture for the spatial data management expert system is described. The system is applied to data from the International Ultraviolet Explorer (IUE) satellite, and results are given.

Use of concept mapping as a facilitative tool to promote learning in pharmacology.

PubMed

Qadir, Farida; Zehra, Tabassum; Khan, Imrana

2011-08-01

To assess whether students find concept mapping a useful learning methodology to conceptualize and organize topics studied in CNS module of Pharmacology; and to evaluate whether addition of concept mapping assignment could help to improve examination scores. An analytical study. College of Dentistry, Jinnah Medical and Dental College, Karachi, Pakistan, from March to May 2009. A class of 50 BDS students was recruited for the study. Two randomly selected groups of 12 students each, prepared concept maps in topics from CNS pharmacology which were displayed and discussed during tutorial sessions. The other two groups (n = 25) following the traditional teaching methodology, served as controls. Scores from best choice questions and short essay questions were compared between the investigational and control groups using the student's t-test with significance at p < 0.05. Feedback obtained after completion of the study was evaluated as percent response. One-best-choice test of the control group showed a mean grade of 57.1 ± 16.7 vs. test group mean of 58.8 ± 13. For the short essay questions, control group obtained a mean of 52.3 ± 18.8 vs. test group mean grade of 53.8 ± 22.5. Both results were not significantly different (p > 0.05). However, feedback about concept mapping showed that the technique helped the students to conceptualize difficult topics in CNS pharmacology (86.36%). Concept mapping was particularly beneficial in preparing for exams as it provided a quick overview of the entire subject (68.68%). Students found concept mapping as a useful pedagogical tool which could potentially be used to acquire meaningful learning in Pharmacology as a supplement to traditional teaching techniques. It was not found beneficial in improving examination grades probably because standard examinations and concept mapping measure different cognitive domains.

Mapping a battlefield simulation onto message-passing parallel architectures

NASA Technical Reports Server (NTRS)

Nicol, David M.

1987-01-01

Perhaps the most critical problem in distributed simulation is that of mapping: without an effective mapping of workload to processors the speedup potential of parallel processing cannot be realized. Mapping a simulation onto a message-passing architecture is especially difficult when the computational workload dynamically changes as a function of time and space; this is exactly the situation faced by battlefield simulations. This paper studies an approach where the simulated battlefield domain is first partitioned into many regions of equal size; typically there are more regions than processors. The regions are then assigned to processors; a processor is responsible for performing all simulation activity associated with the regions. The assignment algorithm is quite simple and attempts to balance load by exploiting locality of workload intensity. The performance of this technique is studied on a simple battlefield simulation implemented on the Flex/32 multiprocessor. Measurements show that the proposed method achieves reasonable processor efficiencies. Furthermore, the method shows promise for use in dynamic remapping of the simulation.

CERT Research Annual Report 2009

DTIC Science & Technology

2009-01-01

Domain Name System (DNS), which maps names to IP addresses, is a vital component of the Internet. Nearly every transaction on the Internet begins by...many different ASNs (Autonomous System Numbers, which map to Internet Service Providers) there are. If there are more than 20, then it is extremely...functions, that is, mappings from their domains to ranges, or inputs to outputs. These mappings are pre-defined as a starting point for the FX

Paleostress Analysis with Reflection Seismic Data: Example from the Songliao Basin, Northeast China

NASA Astrophysics Data System (ADS)

Liu, G.; Persaud, P.; Zhang, Y.

2017-12-01

Currently paleostress inversion using fault-slip data is a well established approach. However, the deformation history contained in folds has not yet been fully utilized to determine the paleostress field. By applying a 2D FFT-based algorithm to a structure or isopach map derived from reflection seismic data, we find a new way of exploiting the information preserved in folds to determine the paleostress. Our method requires that the strata have a large areal extent and are well preserved. After pre-processing the maps, we find that in the frequency-wavenumber (F-K) domain, folds with similar strikes are grouped into spectrum belts. Each belt parallels the short axis of the fold group and can therefore indicate the direction of the associated maximum horizontal stress. Some information on the relative chronology of stresses can be deduced by comparing the structure and isopach spectrum maps, e.g., if the structure spectrum map has one more spectrum belt than that of the isopach map (an approximate paleo-structure map of the corresponding stratum), we can conclude that the indicated stress postdated the deposition of the stratum. We selected three Late Cretaceous strata from a 3D seismic survey located in the intracontinental Songliao Basin, northeast China. The Songliao has experienced four episodes of deformation: mantle upwelling, rifting, postrift thermal subsidence and structural inversion (Feng et al., 2009). The selected strata were deposited during the third stage. Three structure and two isopach maps were decomposed in the F-K domain. Spectral analysis of the lower isopach map shows eight paleostress directions. We also identify a ninth paleostress in addition to the previous eight from the structure maps and the upper isopach map. The eight stress directions that exist in both the isopach and structure maps may have been active throughout the time period spanned by the strata. We interpret the ninth paleostress as being active after the deposition of the lower stratum. The derived paleostress field fits well with the interpretations of other workers and provides more accurate stress directions and chronology. We further apply this technique to the Central Sichuan basin, southwest China, and confirm the multi-directional compressional tectonics of that basin.

Structural sensitivity of x-ray Bragg projection ptychography to domain patterns in epitaxial thin films

NASA Astrophysics Data System (ADS)

Hruszkewycz, S. O.; Zhang, Q.; Holt, M. V.; Highland, M. J.; Evans, P. G.; Fuoss, P. H.

2016-10-01

Bragg projection ptychography (BPP) is a coherent diffraction imaging technique capable of mapping the spatial distribution of the Bragg structure factor in nanostructured thin films. Here, we show that, because these images are projections, the structural sensitivity of the resulting images depends on the film thickness and the aspect ratio and orientation of the features of interest and that image interpretation depends on these factors. We model changes in contrast in the BPP reconstructions of simulated PbTiO3 ferroelectric thin films with meandering 180∘ stripe domains as a function of film thickness, discuss their origin, and comment on the implication of these factors on the design of BPP experiments of general nanostructured films.

Infrared Imaging Tools for Diagnostic Applications in Dermatology.

PubMed

Gurjarpadhye, Abhijit Achyut; Parekh, Mansi Bharat; Dubnika, Arita; Rajadas, Jayakumar; Inayathullah, Mohammed

Infrared (IR) imaging is a collection of non-invasive imaging techniques that utilize the IR domain of the electromagnetic spectrum for tissue assessment. A subset of these techniques construct images using back-reflected light, while other techniques rely on detection of IR radiation emitted by the tissue as a result of its temperature. Modern IR detectors sense thermal emissions and produce a heat map of surface temperature distribution in tissues. Thus, the IR spectrum offers a variety of imaging applications particularly useful in clinical diagnostic area, ranging from high-resolution, depth-resolved visualization of tissue to temperature variation assessment. These techniques have been helpful in the diagnosis of many medical conditions including skin/breast cancer, arthritis, allergy, burns, and others. In this review, we discuss current roles of IR-imaging techniques for diagnostic applications in dermatology with an emphasis on skin cancer, allergies, blisters, burns and wounds.

Association between lesion location and language function in adult glioma using voxel-based lesion-symptom mapping.

PubMed

Banerjee, Pia; Leu, Kevin; Harris, Robert J; Cloughesy, Timothy F; Lai, Albert; Nghiemphu, Phioanh L; Pope, Whitney B; Bookheimer, Susan Y; Ellingson, Benjamin M

2015-01-01

Management of language difficulties is an important aspect of clinical care for glioma patients, and accurately identifying the possible language deficits in patients based on lesion location would be beneficial to clinicians. To that end, we examined the relationship between lesion presence and language performance on tests of receptive language and expressive language using a highly specific voxel-based lesion-symptom mapping (VLSM) approach in glioma patients. 98 adults with primary glioma, who were pre-surgical candidates, were administered seven neurocognitive tests within the domains of receptive language and expressive language. The association between language performance and lesion presence was examined using VLSM. Statistical parametric maps were created for each test, and composite maps for both receptive language and expressive language were created to display the significant voxels common to all tests within these language domains. We identified clusters of voxels with a significant relationship between lesion presence and language performance. All tasks were associated with several white matter pathways. The receptive language tasks were additionally all associated with regions primarily within the lateral temporal lobe and medial temporal lobe. In contrast, the expressive language tasks shared little overlap, despite each task being independently associated with large anatomic areas. Our findings identify the key anatomic structures involved in language functioning in adult glioma patients using an innovative lesion analysis technique and suggest that expressive language abilities may be more task-dependent and distributed than receptive language abilities.

Facilitated assignment of large protein NMR signals with covariance sequential spectra using spectral derivatives.

PubMed

Harden, Bradley J; Nichols, Scott R; Frueh, Dominique P

2014-09-24

Nuclear magnetic resonance (NMR) studies of larger proteins are hampered by difficulties in assigning NMR resonances. Human intervention is typically required to identify NMR signals in 3D spectra, and subsequent procedures depend on the accuracy of this so-called peak picking. We present a method that provides sequential connectivities through correlation maps constructed with covariance NMR, bypassing the need for preliminary peak picking. We introduce two novel techniques to minimize false correlations and merge the information from all original 3D spectra. First, we take spectral derivatives prior to performing covariance to emphasize coincident peak maxima. Second, we multiply covariance maps calculated with different 3D spectra to destroy erroneous sequential correlations. The maps are easy to use and can readily be generated from conventional triple-resonance experiments. Advantages of the method are demonstrated on a 37 kDa nonribosomal peptide synthetase domain subject to spectral overlap.

A New Deep Learning Model for Fault Diagnosis with Good Anti-Noise and Domain Adaptation Ability on Raw Vibration Signals

PubMed Central

Zhang, Wei; Peng, Gaoliang; Li, Chuanhao; Chen, Yuanhang; Zhang, Zhujun

2017-01-01

Intelligent fault diagnosis techniques have replaced time-consuming and unreliable human analysis, increasing the efficiency of fault diagnosis. Deep learning models can improve the accuracy of intelligent fault diagnosis with the help of their multilayer nonlinear mapping ability. This paper proposes a novel method named Deep Convolutional Neural Networks with Wide First-layer Kernels (WDCNN). The proposed method uses raw vibration signals as input (data augmentation is used to generate more inputs), and uses the wide kernels in the first convolutional layer for extracting features and suppressing high frequency noise. Small convolutional kernels in the preceding layers are used for multilayer nonlinear mapping. AdaBN is implemented to improve the domain adaptation ability of the model. The proposed model addresses the problem that currently, the accuracy of CNN applied to fault diagnosis is not very high. WDCNN can not only achieve 100% classification accuracy on normal signals, but also outperform the state-of-the-art DNN model which is based on frequency features under different working load and noisy environment conditions. PMID:28241451

Wavelength selection method with standard deviation: application to pulse oximetry.

PubMed

Vazquez-Jaccaud, Camille; Paez, Gonzalo; Strojnik, Marija

2011-07-01

Near-infrared spectroscopy provides useful biological information after the radiation has penetrated through the tissue, within the therapeutic window. One of the significant shortcomings of the current applications of spectroscopic techniques to a live subject is that the subject may be uncooperative and the sample undergoes significant temporal variations, due to his health status that, from radiometric point of view, introduce measurement noise. We describe a novel wavelength selection method for monitoring, based on a standard deviation map, that allows low-noise sensitivity. It may be used with spectral transillumination, transmission, or reflection signals, including those corrupted by noise and unavoidable temporal effects. We apply it to the selection of two wavelengths for the case of pulse oximetry. Using spectroscopic data, we generate a map of standard deviation that we propose as a figure-of-merit in the presence of the noise introduced by the living subject. Even in the presence of diverse sources of noise, we identify four wavelength domains with standard deviation, minimally sensitive to temporal noise, and two wavelengths domains with low sensitivity to temporal noise.

Orthonormal vector polynomials in a unit circle, Part I: Basis set derived from gradients of Zernike polynomials.

PubMed

Zhao, Chunyu; Burge, James H

2007-12-24

Zernike polynomials provide a well known, orthogonal set of scalar functions over a circular domain, and are commonly used to represent wavefront phase or surface irregularity. A related set of orthogonal functions is given here which represent vector quantities, such as mapping distortion or wavefront gradient. These functions are generated from gradients of Zernike polynomials, made orthonormal using the Gram- Schmidt technique. This set provides a complete basis for representing vector fields that can be defined as a gradient of some scalar function. It is then efficient to transform from the coefficients of the vector functions to the scalar Zernike polynomials that represent the function whose gradient was fit. These new vector functions have immediate application for fitting data from a Shack-Hartmann wavefront sensor or for fitting mapping distortion for optical testing. A subsequent paper gives an additional set of vector functions consisting only of rotational terms with zero divergence. The two sets together provide a complete basis that can represent all vector distributions in a circular domain.

Macromolecular target prediction by self-organizing feature maps.

PubMed

Schneider, Gisbert; Schneider, Petra

2017-03-01

Rational drug discovery would greatly benefit from a more nuanced appreciation of the activity of pharmacologically active compounds against a diverse panel of macromolecular targets. Already, computational target-prediction models assist medicinal chemists in library screening, de novo molecular design, optimization of active chemical agents, drug re-purposing, in the spotting of potential undesired off-target activities, and in the 'de-orphaning' of phenotypic screening hits. The self-organizing map (SOM) algorithm has been employed successfully for these and other purposes. Areas covered: The authors recapitulate contemporary artificial neural network methods for macromolecular target prediction, and present the basic SOM algorithm at a conceptual level. Specifically, they highlight consensus target-scoring by the employment of multiple SOMs, and discuss the opportunities and limitations of this technique. Expert opinion: Self-organizing feature maps represent a straightforward approach to ligand clustering and classification. Some of the appeal lies in their conceptual simplicity and broad applicability domain. Despite known algorithmic shortcomings, this computational target prediction concept has been proven to work in prospective settings with high success rates. It represents a prototypic technique for future advances in the in silico identification of the modes of action and macromolecular targets of bioactive molecules.

A fully automatic three-step liver segmentation method on LDA-based probability maps for multiple contrast MR images.

PubMed

Gloger, Oliver; Kühn, Jens; Stanski, Adam; Völzke, Henry; Puls, Ralf

2010-07-01

Automatic 3D liver segmentation in magnetic resonance (MR) data sets has proven to be a very challenging task in the domain of medical image analysis. There exist numerous approaches for automatic 3D liver segmentation on computer tomography data sets that have influenced the segmentation of MR images. In contrast to previous approaches to liver segmentation in MR data sets, we use all available MR channel information of different weightings and formulate liver tissue and position probabilities in a probabilistic framework. We apply multiclass linear discriminant analysis as a fast and efficient dimensionality reduction technique and generate probability maps then used for segmentation. We develop a fully automatic three-step 3D segmentation approach based upon a modified region growing approach and a further threshold technique. Finally, we incorporate characteristic prior knowledge to improve the segmentation results. This novel 3D segmentation approach is modularized and can be applied for normal and fat accumulated liver tissue properties. Copyright 2010 Elsevier Inc. All rights reserved.

Geological mapping potential of computer-enhanced images from the Shuttle Imaging Radar - Lisbon Valley Anticline, Utah

NASA Technical Reports Server (NTRS)

Curlis, J. D.; Frost, V. S.; Dellwig, L. F.

1986-01-01

Computer-enhancement techniques applied to the SIR-A data from the Lisbon Valley area in the northern portion of the Paradox basin increased the value of the imagery in the development of geologically useful maps. The enhancement techniques include filtering to remove image speckle from the SIR-A data and combining these data with Landsat multispectral scanner data. A method well-suited for the combination of the data sets utilized a three-dimensional domain defined by intensity-hue-saturation (IHS) coordinates. Such a system allows the Landsat data to modulate image intensity, while the SIR-A data control image hue and saturation. Whereas the addition of Landsat data to the SIR-A image by means of a pixel-by-pixel ratio accentuated textural variations within the image, the addition of color to the combined images enabled isolation of areas in which gray-tone contrast was minimal. This isolation resulted in a more precise definition of stratigraphic units.

NeuroLines: A Subway Map Metaphor for Visualizing Nanoscale Neuronal Connectivity.

PubMed

Al-Awami, Ali K; Beyer, Johanna; Strobelt, Hendrik; Kasthuri, Narayanan; Lichtman, Jeff W; Pfister, Hanspeter; Hadwiger, Markus

2014-12-01

We present NeuroLines, a novel visualization technique designed for scalable detailed analysis of neuronal connectivity at the nanoscale level. The topology of 3D brain tissue data is abstracted into a multi-scale, relative distance-preserving subway map visualization that allows domain scientists to conduct an interactive analysis of neurons and their connectivity. Nanoscale connectomics aims at reverse-engineering the wiring of the brain. Reconstructing and analyzing the detailed connectivity of neurons and neurites (axons, dendrites) will be crucial for understanding the brain and its development and diseases. However, the enormous scale and complexity of nanoscale neuronal connectivity pose big challenges to existing visualization techniques in terms of scalability. NeuroLines offers a scalable visualization framework that can interactively render thousands of neurites, and that supports the detailed analysis of neuronal structures and their connectivity. We describe and analyze the design of NeuroLines based on two real-world use-cases of our collaborators in developmental neuroscience, and investigate its scalability to large-scale neuronal connectivity data.

Biologically inspired intelligent decision making

PubMed Central

Manning, Timmy; Sleator, Roy D; Walsh, Paul

2014-01-01

Artificial neural networks (ANNs) are a class of powerful machine learning models for classification and function approximation which have analogs in nature. An ANN learns to map stimuli to responses through repeated evaluation of exemplars of the mapping. This learning approach results in networks which are recognized for their noise tolerance and ability to generalize meaningful responses for novel stimuli. It is these properties of ANNs which make them appealing for applications to bioinformatics problems where interpretation of data may not always be obvious, and where the domain knowledge required for deductive techniques is incomplete or can cause a combinatorial explosion of rules. In this paper, we provide an introduction to artificial neural network theory and review some interesting recent applications to bioinformatics problems. PMID:24335433

Sensitivity analysis of consumption cycles

NASA Astrophysics Data System (ADS)

Jungeilges, Jochen; Ryazanova, Tatyana; Mitrofanova, Anastasia; Popova, Irina

2018-05-01

We study the special case of a nonlinear stochastic consumption model taking the form of a 2-dimensional, non-invertible map with an additive stochastic component. Applying the concept of the stochastic sensitivity function and the related technique of confidence domains, we establish the conditions under which the system's complex consumption attractor is likely to become observable. It is shown that the level of noise intensities beyond which the complex consumption attractor is likely to be observed depends on the weight given to past consumption in an individual's preference adjustment.

Femtosecond timing measurement and control using ultrafast organic thin films

NASA Astrophysics Data System (ADS)

Naruse, Makoto; Mitsu, Hiroyuki; Furuki, Makoto; Iwasa, Izumi; Sato, Yasuhiro; Tatsuura, Satoshi; Tian, Minquan

2003-12-01

We show a femtosecond timing measurement and control technique using a squarylium dye J-aggregate film, which is an organic thin film that acts as an ultrafast two-dimensional optical switch. Optical pulse timing is directly mapped to space-domain position on the film, and the large area and ultrafast response offer a femtosecond-resolved, large dynamic range, real-time, multichannel timing measurement capability. A timing fluctuation (jitter, wander, and skew) reduction architecture is presented and experimentally demonstrated.

Regional Geological Mapping in the Graham Land of Antarctic Peninsula Using LANDSAT-8 Remote Sensing Data

NASA Astrophysics Data System (ADS)

Pour, A. B.; Hashim, M.; Park, Y.

2017-10-01

Geological investigations in Antarctica confront many difficulties due to its remoteness and extreme environmental conditions. In this study, the applications of Landsat-8 data were investigated to extract geological information for lithological and alteration mineral mapping in poorly exposed lithologies in inaccessible domains such in Antarctica. The north-eastern Graham Land, Antarctic Peninsula (AP) was selected in this study to conduct a satellite-based remote sensing mapping technique. Continuum Removal (CR) spectral mapping tool and Independent Components Analysis (ICA) were applied to Landsat-8 spectral bands to map poorly exposed lithologies at regional scale. Pixels composed of distinctive absorption features of alteration mineral assemblages associated with poorly exposed lithological units were detected by applying CR mapping tool to VNIR and SWIR bands of Landsat-8.Pixels related to Si-O bond emission minima features were identified using CR mapping tool to TIR bands in poorly mapped andunmapped zones in north-eastern Graham Land at regional scale. Anomaly pixels in the ICA image maps related to spectral featuresof Al-O-H, Fe, Mg-O-H and CO3 groups and well-constrained lithological attributions from felsic to mafic rocks were detectedusing VNIR, SWIR and TIR datasets of Landsat-8. The approach used in this study performed very well for lithological andalteration mineral mapping with little available geological data or without prior information of the study region.

3DIANA: 3D Domain Interaction Analysis: A Toolbox for Quaternary Structure Modeling

PubMed Central

Segura, Joan; Sanchez-Garcia, Ruben; Tabas-Madrid, Daniel; Cuenca-Alba, Jesus; Sorzano, Carlos Oscar S.; Carazo, Jose Maria

2016-01-01

Electron microscopy (EM) is experiencing a revolution with the advent of a new generation of Direct Electron Detectors, enabling a broad range of large and flexible structures to be resolved well below 1 nm resolution. Although EM techniques are evolving to the point of directly obtaining structural data at near-atomic resolution, for many molecules the attainable resolution might not be enough to propose high-resolution structural models. However, accessing information on atomic coordinates is a necessary step toward a deeper understanding of the molecular mechanisms that allow proteins to perform specific tasks. For that reason, methods for the integration of EM three-dimensional maps with x-ray and NMR structural data are being developed, a modeling task that is normally referred to as fitting, resulting in the so called hybrid models. In this work, we present a novel application—3DIANA—specially targeted to those cases in which the EM map resolution is medium or low and additional experimental structural information is scarce or even lacking. In this way, 3DIANA statistically evaluates proposed/potential contacts between protein domains, presents a complete catalog of both structurally resolved and predicted interacting regions involving these domains and, finally, suggests structural templates to model the interaction between them. The evaluation of the proposed interactions is computed with DIMERO, a new method that scores physical binding sites based on the topology of protein interaction networks, which has recently shown the capability to increase by 200% the number of domain-domain interactions predicted in interactomes as compared to previous approaches. The new application displays the information at a sequence and structural level and is accessible through a web browser or as a Chimera plugin at http://3diana.cnb.csic.es. PMID:26772592

Analysis of spatial distribution of land cover maps accuracy

NASA Astrophysics Data System (ADS)

Khatami, R.; Mountrakis, G.; Stehman, S. V.

2017-12-01

Land cover maps have become one of the most important products of remote sensing science. However, classification errors will exist in any classified map and affect the reliability of subsequent map usage. Moreover, classification accuracy often varies over different regions of a classified map. These variations of accuracy will affect the reliability of subsequent analyses of different regions based on the classified maps. The traditional approach of map accuracy assessment based on an error matrix does not capture the spatial variation in classification accuracy. Here, per-pixel accuracy prediction methods are proposed based on interpolating accuracy values from a test sample to produce wall-to-wall accuracy maps. Different accuracy prediction methods were developed based on four factors: predictive domain (spatial versus spectral), interpolation function (constant, linear, Gaussian, and logistic), incorporation of class information (interpolating each class separately versus grouping them together), and sample size. Incorporation of spectral domain as explanatory feature spaces of classification accuracy interpolation was done for the first time in this research. Performance of the prediction methods was evaluated using 26 test blocks, with 10 km × 10 km dimensions, dispersed throughout the United States. The performance of the predictions was evaluated using the area under the curve (AUC) of the receiver operating characteristic. Relative to existing accuracy prediction methods, our proposed methods resulted in improvements of AUC of 0.15 or greater. Evaluation of the four factors comprising the accuracy prediction methods demonstrated that: i) interpolations should be done separately for each class instead of grouping all classes together; ii) if an all-classes approach is used, the spectral domain will result in substantially greater AUC than the spatial domain; iii) for the smaller sample size and per-class predictions, the spectral and spatial domain yielded similar AUC; iv) for the larger sample size (i.e., very dense spatial sample) and per-class predictions, the spatial domain yielded larger AUC; v) increasing the sample size improved accuracy predictions with a greater benefit accruing to the spatial domain; and vi) the function used for interpolation had the smallest effect on AUC.

Integrating natural language processing and web GIS for interactive knowledge domain visualization

NASA Astrophysics Data System (ADS)

Du, Fangming

Recent years have seen a powerful shift towards data-rich environments throughout society. This has extended to a change in how the artifacts and products of scientific knowledge production can be analyzed and understood. Bottom-up approaches are on the rise that combine access to huge amounts of academic publications with advanced computer graphics and data processing tools, including natural language processing. Knowledge domain visualization is one of those multi-technology approaches, with its aim of turning domain-specific human knowledge into highly visual representations in order to better understand the structure and evolution of domain knowledge. For example, network visualizations built from co-author relations contained in academic publications can provide insight on how scholars collaborate with each other in one or multiple domains, and visualizations built from the text content of articles can help us understand the topical structure of knowledge domains. These knowledge domain visualizations need to support interactive viewing and exploration by users. Such spatialization efforts are increasingly looking to geography and GIS as a source of metaphors and practical technology solutions, even when non-georeferenced information is managed, analyzed, and visualized. When it comes to deploying spatialized representations online, web mapping and web GIS can provide practical technology solutions for interactive viewing of knowledge domain visualizations, from panning and zooming to the overlay of additional information. This thesis presents a novel combination of advanced natural language processing - in the form of topic modeling - with dimensionality reduction through self-organizing maps and the deployment of web mapping/GIS technology towards intuitive, GIS-like, exploration of a knowledge domain visualization. A complete workflow is proposed and implemented that processes any corpus of input text documents into a map form and leverages a web application framework to let users explore knowledge domain maps interactively. This workflow is implemented and demonstrated for a data set of more than 66,000 conference abstracts.

Analysis of improved government geological map information for mineral exploration: Incorporating efficiency, productivity, effectiveness, and risk considerations

USGS Publications Warehouse

Bernknopf, R.L.; Wein, A.M.; St-Onge, M. R.; Lucas, S.B.

2007-01-01

This bulletin/professional paper focuses on the value of geoscientific information and knowledge, as provided in published government bedrock geological maps, to the mineral exploration sector. An economic model is developed that uses an attribute- ranking approach to convert geological maps into domains of mineral favourability. Information about known deposits in these (or analogous) favourability domains allow the calculation of exploration search statistics that provide input into measures of exploration efficiency, productivity, effectiveness, risk, and cost stemming from the use of the published geological maps. Two case studies, the Flin Flon Belt (Manitoba and Saskatchewan) and the south Baffin Island area (Nunavut), demonstrate that updated, finer resolution maps can be used to identify more exploration campaign options, and campaigns thats are more efficient, more effective, and less risky than old, coarser resolution maps when used as a guide for mineral exploration. The Flin Flon Belt study illustrates that an updated, coarser resolution bedrock map enables improved mineral exploration efficiency, productivity, and effectiveness by locating 60% more targets and supporting an exploration campaign that is 44% more efficient. Refining the map resolution provides an additional 17% reduction in search effort across all favourable domains and a 55% reduction in search effort in the most favourable domain. The south Baffin Island case study projects a 40% increase in expected targets and a 27% reduction in search effort when the updated, finer resolution map is used in lieu of the old, coarser resolution map. On southern Baffin Island, the economic value of the up dated map ranges from CAN$2.28 million to CAN$15.21 million, which can be compared to the CAN$1.86 million that it cost to produce the map (a multiplier effect of up to eight).

Characteristic Lifelength of Coherent Structure in the Turbulent Boundary Layer

NASA Technical Reports Server (NTRS)

Palumbo, Daniel L.

2006-01-01

A characteristic lifelength is defined by which a Gaussian distribution is fit to data correlated over a 3 sensor array sampling streamwise sidewall pressure. The data were acquired at subsonic, transonic and supersonic speeds aboard a Tu-144. Lifelengths are estimated using the cross spectrum and are shown to compare favorably with Efimtsov's prediction of correlation space scales. Lifelength distributions are computed in the time/frequency domain using an interval correlation technique on the continuous wavelet transform of the original time data. The median values of the lifelength distributions are found to be very close to the frequency averaged result. The interval correlation technique is shown to allow the retrieval and inspection of the original time data of each event in the lifelength distribution, thus providing a means to locate and study the nature of the coherent structure in the turbulent boundary layer. The lifelength data can be converted to lifetimes using the convection velocity. The lifetime of events in the time/frequency domain are displayed in Lifetime Maps. The primary purpose of the paper is to validate these new analysis techniques so that they can be used with confidence to further characterize coherent structure in the turbulent boundary layer.

Instructional Curriculum Mapping.

ERIC Educational Resources Information Center

Wager, Walter

Instructional Curriculum Mapping (ICM) is a set of guidelines for diagramming the interrelationships among objectives from different domains of learning. Five major learning domains are identified: (1) intellectual skills; (2) cognitive strategies; (3) verbal information; (4) motor skills; and (5) attitudes. This paper examines the functional…

Understanding neurodynamical systems via Fuzzy Symbolic Dynamics.

PubMed

Dobosz, Krzysztof; Duch, Włodzisław

2010-05-01

Neurodynamical systems are characterized by a large number of signal streams, measuring activity of individual neurons, local field potentials, aggregated electrical (EEG) or magnetic potentials (MEG), oxygen use (fMRI) or activity of simulated neurons. Various basis set decomposition techniques are used to analyze such signals, trying to discover components that carry meaningful information, but these techniques tell us little about the global activity of the whole system. A novel technique called Fuzzy Symbolic Dynamics (FSD) is introduced to help in understanding of the multidimensional dynamical system's behavior. It is based on a fuzzy partitioning of the signal space that defines a non-linear mapping of the system's trajectory to the low-dimensional space of membership function activations. This allows for visualization of the trajectory showing various aspects of observed signals that may be difficult to discover looking at individual components, or to notice otherwise. FSD mapping can be applied to raw signals, transformed signals (for example, ICA components), or to signals defined in the time-frequency domain. To illustrate the method two FSD visualizations are presented: a model system with artificial radial oscillatory sources, and the output layer (50 neurons) of Respiratory Rhythm Generator (RRG) composed of 300 spiking neurons. 2009 Elsevier Ltd. All rights reserved.

Ultrafast Method for the Analysis of Fluorescence Lifetime Imaging Microscopy Data Based on the Laguerre Expansion Technique

PubMed Central

Jo, Javier A.; Fang, Qiyin; Marcu, Laura

2007-01-01

We report a new deconvolution method for fluorescence lifetime imaging microscopy (FLIM) based on the Laguerre expansion technique. The performance of this method was tested on synthetic and real FLIM images. The following interesting properties of this technique were demonstrated. 1) The fluorescence intensity decay can be estimated simultaneously for all pixels, without a priori assumption of the decay functional form. 2) The computation speed is extremely fast, performing at least two orders of magnitude faster than current algorithms. 3) The estimated maps of Laguerre expansion coefficients provide a new domain for representing FLIM information. 4) The number of images required for the analysis is relatively small, allowing reduction of the acquisition time. These findings indicate that the developed Laguerre expansion technique for FLIM analysis represents a robust and extremely fast deconvolution method that enables practical applications of FLIM in medicine, biology, biochemistry, and chemistry. PMID:19444338

An Approach to Quad Meshing Based On Cross Valued Maps and the Ginzburg-Landau Theory

DOE Office of Scientific and Technical Information (OSTI.GOV)

Viertel, Ryan; Osting, Braxton

2017-08-01

A generalization of vector fields, referred to as N-direction fields or cross fields when N=4, has been recently introduced and studied for geometry processing, with applications in quadrilateral (quad) meshing, texture mapping, and parameterization. We make the observation that cross field design for two-dimensional quad meshing is related to the well-known Ginzburg-Landau problem from mathematical physics. This identification yields a variety of theoretical tools for efficiently computing boundary-aligned quad meshes, with provable guarantees on the resulting mesh, for example, the number of mesh defects and bounds on the defect locations. The procedure for generating the quad mesh is to (i)more » find a complex-valued "representation" field that minimizes the Dirichlet energy subject to a boundary constraint, (ii) convert the representation field into a boundary-aligned, smooth cross field, (iii) use separatrices of the cross field to partition the domain into four sided regions, and (iv) mesh each of these four-sided regions using standard techniques. Under certain assumptions on the geometry of the domain, we prove that this procedure can be used to produce a cross field whose separatrices partition the domain into four sided regions. To solve the energy minimization problem for the representation field, we use an extension of the Merriman-Bence-Osher (MBO) threshold dynamics method, originally conceived as an algorithm to simulate motion by mean curvature, to minimize the Ginzburg-Landau energy for the optimal representation field. Lastly, we demonstrate the method on a variety of test domains.« less

Structural sensitivity of x-ray Bragg projection ptychography to domain patterns in epitaxial thin films

DOE PAGES

Hruszkewycz, S. O.; Zhang, Q.; Holt, M. V.; ...

2016-10-04

Bragg projection ptychography (BPP) is a coherent diffraction imaging technique capable of mapping the spatial distribution of the Bragg structure factor in nanostructured thin films. Here, we show that, because these images are projections, the structural sensitivity of the resulting images depends on the film thickness and the aspect ratio and orientation of the features of interest and that image interpretation depends on these factors. Lastly, we model changes in contrast in the BPP reconstructions of simulated PbTiO 3 ferroelectric thin films with meandering 180° stripe domains as a function of film thickness, discuss their origin, and comment on themore » implication of these factors on the design of BPP experiments of general nanostructured films.« less

On Probability Domains IV

NASA Astrophysics Data System (ADS)

Frič, Roman; Papčo, Martin

2017-12-01

Stressing a categorical approach, we continue our study of fuzzified domains of probability, in which classical random events are replaced by measurable fuzzy random events. In operational probability theory (S. Bugajski) classical random variables are replaced by statistical maps (generalized distribution maps induced by random variables) and in fuzzy probability theory (S. Gudder) the central role is played by observables (maps between probability domains). We show that to each of the two generalized probability theories there corresponds a suitable category and the two resulting categories are dually equivalent. Statistical maps and observables become morphisms. A statistical map can send a degenerated (pure) state to a non-degenerated one —a quantum phenomenon and, dually, an observable can map a crisp random event to a genuine fuzzy random event —a fuzzy phenomenon. The dual equivalence means that the operational probability theory and the fuzzy probability theory coincide and the resulting generalized probability theory has two dual aspects: quantum and fuzzy. We close with some notes on products and coproducts in the dual categories.

Optimizing spectral wave estimates with adjoint-based sensitivity maps

NASA Astrophysics Data System (ADS)

Orzech, Mark; Veeramony, Jay; Flampouris, Stylianos

2014-04-01

A discrete numerical adjoint has recently been developed for the stochastic wave model SWAN. In the present study, this adjoint code is used to construct spectral sensitivity maps for two nearshore domains. The maps display the correlations of spectral energy levels throughout the domain with the observed energy levels at a selected location or region of interest (LOI/ROI), providing a full spectrum of values at all locations in the domain. We investigate the effectiveness of sensitivity maps based on significant wave height ( H s ) in determining alternate offshore instrument deployment sites when a chosen nearshore location or region is inaccessible. Wave and bathymetry datasets are employed from one shallower, small-scale domain (Duck, NC) and one deeper, larger-scale domain (San Diego, CA). The effects of seasonal changes in wave climate, errors in bathymetry, and multiple assimilation points on sensitivity map shapes and model performance are investigated. Model accuracy is evaluated by comparing spectral statistics as well as with an RMS skill score, which estimates a mean model-data error across all spectral bins. Results indicate that data assimilation from identified high-sensitivity alternate locations consistently improves model performance at nearshore LOIs, while assimilation from low-sensitivity locations results in lesser or no improvement. Use of sub-sampled or alongshore-averaged bathymetry has a domain-specific effect on model performance when assimilating from a high-sensitivity alternate location. When multiple alternate assimilation locations are used from areas of lower sensitivity, model performance may be worse than with a single, high-sensitivity assimilation point.

Texturing of continuous LOD meshes with the hierarchical texture atlas

NASA Astrophysics Data System (ADS)

Birkholz, Hermann

2006-02-01

For the rendering of detailed virtual environments, trade-offs have to be made between image quality and rendering time. An immersive experience of virtual reality always demands high frame-rates with the best reachable image qual-ity. Continuous Level of Detail (cLoD) triangle-meshes provide an continuous spectrum of detail for a triangle mesh that can be used to create view-dependent approximations of the environment in real-time. This enables the rendering with a constant number of triangles and thus with constant frame-rates. Normally the construction of such cLoD mesh representations leads to the loss of all texture information of the original mesh. To overcome this problem, a parameter domain can be created, in order to map the surface properties (colour, texture, normal) to it. This parameter domain can be used to map the surface properties back to arbitrary approximations of the original mesh. The parameter domain is often a simplified version of the mesh to be parameterised. This limits the reachable simplification to the domain mesh which has to map the surface of the original mesh with the least possible stretch. In this paper, a hierarchical domain mesh is presented, that scales between very coarse domain meshes and good property-mapping.

Hierarchical Bayesian method for mapping biogeochemical hot spots using induced polarization imaging

DOE PAGES

Wainwright, Haruko M.; Flores Orozco, Adrian; Bucker, Matthias; ...

2016-01-29

In floodplain environments, a naturally reduced zone (NRZ) is considered to be a common biogeochemical hot spot, having distinct microbial and geochemical characteristics. Although important for understanding their role in mediating floodplain biogeochemical processes, mapping the subsurface distribution of NRZs over the dimensions of a floodplain is challenging, as conventional wellbore data are typically spatially limited and the distribution of NRZs is heterogeneous. In this work, we present an innovative methodology for the probabilistic mapping of NRZs within a three-dimensional (3-D) subsurface domain using induced polarization imaging, which is a noninvasive geophysical technique. Measurements consist of surface geophysical surveys andmore » drilling-recovered sediments at the U.S. Department of Energy field site near Rifle, CO (USA). Inversion of surface time domain-induced polarization (TDIP) data yielded 3-D images of the complex electrical resistivity, in terms of magnitude and phase, which are associated with mineral precipitation and other lithological properties. By extracting the TDIP data values colocated with wellbore lithological logs, we found that the NRZs have a different distribution of resistivity and polarization from the other aquifer sediments. To estimate the spatial distribution of NRZs, we developed a Bayesian hierarchical model to integrate the geophysical and wellbore data. In addition, the resistivity images were used to estimate hydrostratigraphic interfaces under the floodplain. Validation results showed that the integration of electrical imaging and wellbore data using a Bayesian hierarchical model was capable of mapping spatially heterogeneous interfaces and NRZ distributions thereby providing a minimally invasive means to parameterize a hydrobiogeochemical model of the floodplain.« less

Spatializing Emotion: No Evidence for a Domain-General Magnitude System.

PubMed

Pitt, Benjamin; Casasanto, Daniel

2017-11-22

People implicitly associate different emotions with different locations in left-right space. Which aspects of emotion do they spatialize, and why? Across many studies people spatialize emotional valence, mapping positive emotions onto their dominant side of space and negative emotions onto their non-dominant side, consistent with theories of metaphorical mental representation. Yet other results suggest a conflicting mapping of emotional intensity (a.k.a., emotional magnitude), according to which people associate more intense emotions with the right and less intense emotions with the left - regardless of their valence; this pattern has been interpreted as support for a domain-general system for representing magnitudes. To resolve the apparent contradiction between these mappings, we first tested whether people implicitly map either valence or intensity onto left-right space, depending on which dimension of emotion they attend to (Experiments 1a, b). When asked to judge emotional valence, participants showed the predicted valence mapping. However, when asked to judge emotional intensity, participants showed no systematic intensity mapping. We then tested an alternative explanation of findings previously interpreted as evidence for an intensity mapping (Experiments 2a, b). These results suggest that previous findings may reflect a left-right mapping of spatial magnitude (i.e., the size of a salient feature of the stimuli) rather than emotion. People implicitly spatialize emotional valence, but, at present, there is no clear evidence for an implicit lateral mapping of emotional intensity. These findings support metaphor theory and challenge the proposal that mental magnitudes are represented by a domain-general metric that extends to the domain of emotion. Copyright © 2017 Cognitive Science Society, Inc.

Biologically inspired intelligent decision making: a commentary on the use of artificial neural networks in bioinformatics.

PubMed

Manning, Timmy; Sleator, Roy D; Walsh, Paul

2014-01-01

Artificial neural networks (ANNs) are a class of powerful machine learning models for classification and function approximation which have analogs in nature. An ANN learns to map stimuli to responses through repeated evaluation of exemplars of the mapping. This learning approach results in networks which are recognized for their noise tolerance and ability to generalize meaningful responses for novel stimuli. It is these properties of ANNs which make them appealing for applications to bioinformatics problems where interpretation of data may not always be obvious, and where the domain knowledge required for deductive techniques is incomplete or can cause a combinatorial explosion of rules. In this paper, we provide an introduction to artificial neural network theory and review some interesting recent applications to bioinformatics problems.

Development and comparison of processing maps of Mg-3Sn-1Ca alloy from data obtained in tension versus compression

NASA Astrophysics Data System (ADS)

Rao, K. P.; Suresh, K.; Prasad, Y. V. R. K.; Hort, N.

2018-01-01

The hot workability of extruded Mg-3Sn-1Ca alloy has been evaluated by developing processing maps with flow stress data from compression and tensile tests with a view to find the effect of the applied state-of-stress. The processing maps developed at a strain of 0.2 are essentially similar irrespective of the mode of deformation - compression or tension, and exhibit three domains in the temperature ranges: (1) 350 - 425 °C, and (2) 450 - 550 °C and (3) 400 - 500 °C, the first two occurring at lower strain rates and the third occurring at higher strain rates. In all the three domains, dynamic recrystallization occurs and is caused by non-basal slip and controlled by lattice self-diffusion in the first and second domains and grain boundary self-diffusion in the third domain. The state-of-stress imposed on the specimen (compression or tension) does not have any significant effect on the processing maps.

Domain Specificity of MAP3K Family Members, MLK and Tak1, for JNK Signaling in Drosophila

PubMed Central

Stronach, Beth; Lennox, Ashley L.; Garlena, Rebecca A.

2014-01-01

A highly diverse set of protein kinases functions as early responders in the mitogen- and stress-activated protein kinase (MAPK/SAPK) signaling pathways. For instance, humans possess 14 MAPK kinase kinases (MAP3Ks) that activate Jun kinase (JNK) signaling downstream. A major challenge is to decipher the selective and redundant functions of these upstream MAP3Ks. Taking advantage of the relative simplicity of Drosophila melanogaster as a model system, we assessed MAP3K signaling specificity in several JNK-dependent processes during development and stress response. Our approach was to generate molecular chimeras between two MAP3K family members, the mixed lineage kinase, Slpr, and the TGF-β activated kinase, Tak1, which share 32% amino acid identity across the kinase domain but otherwise differ in sequence and domain structure, and then test the contributions of various domains for protein localization, complementation of mutants, and activation of signaling. We found that overexpression of the wild-type kinases stimulated JNK signaling in alternate contexts, so cells were capable of responding to both MAP3Ks, but with distinct outcomes. Relative to wild-type, the catalytic domain swaps compensated weakly or not at all, despite having a shared substrate, the JNK kinase Hep. Tak1 C-terminal domain-containing constructs were inhibitory in Tak1 signaling contexts, including tumor necrosis factor-dependent cell death and innate immune signaling; however, depressing antimicrobial gene expression did not necessarily cause phenotypic susceptibility to infection. These same constructs were neutral in the context of Slpr-dependent developmental signaling, reflecting differential subcellular protein localization and by inference, point of activation. Altogether, our findings suggest that the selective deployment of a particular MAP3K can be attributed in part to its inherent sequence differences, cellular localization, and binding partner availability. PMID:24429281

Charge collection kinetics on ferroelectric polymer surface using charge gradient microscopy

DOE PAGES

Choi, Yoon-Young; Tong, Sheng; Ducharme, Stephen P.; ...

2016-05-03

Here, a charge gradient microscopy (CGM) probe was used to collect surface screening charges on poly(vinylidene fluoride-trifluoroethylene) [P(VDF-TrFE)] thin films. These charges are naturally formed on unscreened ferroelectric domains in ambient condition. The CGM data were used to map the local electric current originating from the collected surface charges on the poled ferroelectric domains in the P(VDF-TrFE) thin films. Both the direction and amount of the collected current were controlled by changing the polarity and area of the poled domains. The endurance of charge collection by rubbing the CGM tip on the polymer film was limited to 20 scan cycles,more » after which the current reduced to almost zero. This degradation was attributed to the increase of the chemical bonding strength between the external screening charges and the polarization charges. Once this degradation mechanism is mitigated, the CGM technique can be applied to efficient energy harvesting devices using polymer ferroelectrics.« less

Solution structure and DNA-binding properties of the C-terminal domain of UvrC from E.coli

PubMed Central

Singh, S.; Folkers, G.E.; Bonvin, A.M.J.J.; Boelens, R.; Wechselberger, R.; Niztayev, A.; Kaptein, R.

2002-01-01

The C-terminal domain of the UvrC protein (UvrC CTD) is essential for 5′ incision in the prokaryotic nucleotide excision repair process. We have determined the three-dimensional structure of the UvrC CTD using heteronuclear NMR techniques. The structure shows two helix–hairpin–helix (HhH) motifs connected by a small connector helix. The UvrC CTD is shown to mediate structure-specific DNA binding. The domain binds to a single-stranded–double-stranded junction DNA, with a strong specificity towards looped duplex DNA that contains at least six unpaired bases per loop (‘bubble DNA’). Using chemical shift perturbation experiments, the DNA-binding surface is mapped to the first hairpin region encompassing the conserved glycine–valine–glycine residues followed by lysine–arginine–arginine, a positively charged surface patch and the second hairpin region consisting of glycine–isoleucine–serine. A model for the protein– DNA complex is proposed that accounts for this specificity. PMID:12426397

Phase-space topography characterization of nonlinear ultrasound waveforms.

PubMed

Dehghan-Niri, Ehsan; Al-Beer, Helem

2018-03-01

Fundamental understanding of ultrasound interaction with material discontinuities having closed interfaces has many engineering applications such as nondestructive evaluation of defects like kissing bonds and cracks in critical structural and mechanical components. In this paper, to analyze the acoustic field nonlinearities due to defects with closed interfaces, the use of a common technique in nonlinear physics, based on a phase-space topography construction of ultrasound waveform, is proposed. The central idea is to complement the "time" and "frequency" domain analyses with the "phase-space" domain analysis of nonlinear ultrasound waveforms. A nonlinear time series method known as pseudo phase-space topography construction is used to construct equivalent phase-space portrait of measured ultrasound waveforms. Several nonlinear models are considered to numerically simulate nonlinear ultrasound waveforms. The phase-space response of the simulated waveforms is shown to provide different topographic information, while the frequency domain shows similar spectral behavior. Thus, model classification can be substantially enhanced in the phase-space domain. Experimental results on high strength aluminum samples show that the phase-space transformation provides a unique detection and classification capabilities. The Poincaré map of the phase-space domain is also used to better understand the nonlinear behavior of ultrasound waveforms. It is shown that the analysis of ultrasound nonlinearities is more convenient and informative in the phase-space domain than in the frequency domain. Copyright © 2017 Elsevier B.V. All rights reserved.

Arabidopsis Microtubule-Associated Protein MAP65-3 Cross-Links Antiparallel Microtubules toward Their Plus Ends in the Phragmoplast via Its Distinct C-Terminal Microtubule Binding Domain[W

PubMed Central

Ho, Chin-Min Kimmy; Lee, Yuh-Ru Julie; Kiyama, Lindsay D.; Dinesh-Kumar, Savithramma P.; Liu, Bo

2012-01-01

Plant cytokinesis is brought about by the phragmoplast, which contains an antiparallel microtubule (MT) array. The MT-associated protein MAP65-3 acts as an MT-bundling factor that specifically cross-links antiparallel MTs near their plus ends. MAP65 family proteins contain an N-terminal dimerization domain and C-terminal MT interaction domain. Compared with other MAP65 isoforms, MAP65-3 contains an extended C terminus. A MT binding site was discovered in the region between amino acids 496 and 588 and found to be essential for the organization of phragmoplast MTs. The frequent cytokinetic failure caused by loss of MAP65-3 was not rescued by ectopic expression of MAP65-1 under the control of the MAP65-3 promoter, indicating nonoverlapping functions between the two isoforms. In the presence of MAP65-3, however, ectopic MAP65-1 appeared in the phragmoplast midline. We show that MAP65-1 could acquire the function of MAP65-3 when the C terminus of MAP65-3, which contains the MT binding site, was grafted to it. Our results also show that MAP65-1 and MAP65-3 may share redundant functions in MT stabilization. Such a stabilization effect was likely brought about by MT binding and bundling. We conclude that MAP65-3 contains a distinct C-terminal MT binding site with a specific role in cross-linking antiparallel MTs toward their plus ends in the phragmoplast. PMID:22570443

[The intervention mapping protocol: A structured process to develop, implement and evaluate health promotion programs].

PubMed

Fassier, J-B; Lamort-Bouché, M; Sarnin, P; Durif-Bruckert, C; Péron, J; Letrilliart, L; Durand, M-J

2016-02-01

Health promotion programs are expected to improve population health and reduce social inequalities in health. However, their theoretical foundations are frequently ill-defined, and their implementation faces many obstacles. The aim of this article is to describe the intervention mapping protocol in health promotion programs planning, used recently in several countries. The challenges of planning health promotion programs are presented, and the six steps of the intervention mapping protocol are described with an example. Based on a literature review, the use of this protocol, its requirements and potential limitations are discussed. The intervention mapping protocol has four essential characteristics: an ecological perspective (person-environment), a participative approach, the use of theoretical models in human and social sciences and the use of scientific evidence. It comprises six steps: conduct a health needs assessment, define change objectives, select theory-based change techniques and practical applications, organize techniques and applications into an intervention program (logic model), plan for program adoption, implementation, and sustainability, and generate an evaluation plan. This protocol was used in different countries and domains such as obesity, tobacco, physical activity, cancer and occupational health. Although its utilization requires resources and a critical stance, this protocol was used to develop interventions which efficacy was demonstrated. The intervention mapping protocol is an integrated process that fits the scientific and practical challenges of health promotion. It could be tested in France as it was used in other countries, in particular to reduce social inequalities in health. Copyright © 2016. Published by Elsevier Masson SAS.

Complementary and conventional medicine: a concept map

PubMed Central

Baldwin, Carol M; Kroesen, Kendall; Trochim, William M; Bell, Iris R

2004-01-01

Background Despite the substantive literature from survey research that has accumulated on complementary and alternative medicine (CAM) in the United States and elsewhere, very little research has been done to assess conceptual domains that CAM and conventional providers would emphasize in CAM survey studies. The objective of this study is to describe and interpret the results of concept mapping with conventional and CAM practitioners from a variety of backgrounds on the topic of CAM. Methods Concept mapping, including free sorts, ratings, and multidimensional scaling was used to organize conceptual domains relevant to CAM into a visual "cluster map." The panel consisted of CAM providers, conventional providers, and university faculty, and was convened to help formulate conceptual domains to guide the development of a CAM survey for use with United States military veterans. Results Eight conceptual clusters were identified: 1) Self-assessment, Self-care, and Quality of Life; 2) Health Status, Health Behaviors; 3) Self-assessment of Health; 4) Practical/Economic/ Environmental Concerns; 5) Needs Assessment; 6) CAM vs. Conventional Medicine; 7) Knowledge of CAM; and 8) Experience with CAM. The clusters suggest panelists saw interactions between CAM and conventional medicine as a critical component of the current medical landscape. Conclusions Concept mapping provided insight into how CAM and conventional providers view the domain of health care, and was shown to be a useful tool in the formulation of CAM-related conceptual domains. PMID:15018623

Accelerating parallel transmit array B1 mapping in high field MRI with slice undersampling and interpolation by kriging.

PubMed

Ferrand, Guillaume; Luong, Michel; Cloos, Martijn A; Amadon, Alexis; Wackernagel, Hans

2014-08-01

Transmit arrays have been developed to mitigate the RF field inhomogeneity commonly observed in high field magnetic resonance imaging (MRI), typically above 3T. To this end, the knowledge of the RF complex-valued B1 transmit-sensitivities of each independent radiating element has become essential. This paper details a method to speed up a currently available B1-calibration method. The principle relies on slice undersampling, slice and channel interleaving and kriging, an interpolation method developed in geostatistics and applicable in many domains. It has been demonstrated that, under certain conditions, kriging gives the best estimator of a field in a region of interest. The resulting accelerated sequence allows mapping a complete set of eight volumetric field maps of the human head in about 1 min. For validation, the accuracy of kriging is first evaluated against a well-known interpolation technique based on Fourier transform as well as to a B1-maps interpolation method presented in the literature. This analysis is carried out on simulated and decimated experimental B1 maps. Finally, the accelerated sequence is compared to the standard sequence on a phantom and a volunteer. The new sequence provides B1 maps three times faster with a loss of accuracy limited potentially to about 5%.

Robust reconstruction of B1 (+) maps by projection into a spherical functions space.

PubMed

Sbrizzi, Alessandro; Hoogduin, Hans; Lagendijk, Jan J; Luijten, Peter; van den Berg, Cornelis A T

2014-01-01

Several parallel transmit MRI techniques require knowledge of the transmit radiofrequency field profiles (B1 (+) ). During the past years, various methods have been developed to acquire this information. Often, these methods suffer from long measurement times and produce maps exhibiting regions with poor signal-to-noise ratio and artifacts. In this article, a model-based reconstruction procedure is introduced that improves the robustness of B1 (+) mapping. The missing information from undersampled B1 (+) maps and the regions of poor signal to noise ratio are reconstructed through projection into the space of spherical functions that arise naturally from the solution of the Helmholtz equations in the spherical coordinate system. As a result, B1 (+) data over a limited range of the field of view/volume is sufficient to reconstruct the B1 (+) over the full spatial domain in a fast and robust way. The same model is exploited to filter the noise of the measured maps. Results from simulations and in vivo measurements confirm the validity of the proposed method. A spherical functions model can well approximate the magnetic fields inside the body with few basis terms. Exploiting this compression capability, B1 (+) maps are reconstructed in regions of unknown or corrupted values. Copyright © 2013 Wiley Periodicals, Inc.

Terahertz wide aperture reflection tomography.

PubMed

Pearce, Jeremy; Choi, Hyeokho; Mittleman, Daniel M; White, Jeff; Zimdars, David

2005-07-01

We describe a powerful imaging modality for terahertz (THz) radiation, THz wide aperture reflection tomography (WART). Edge maps of an object's cross section are reconstructed from a series of time-domain reflection measurements at different viewing angles. Each measurement corresponds to a parallel line projection of the object's cross section. The filtered backprojection algorithm is applied to recover the image from the projection data. To our knowledge, this is the first demonstration of a reflection computed tomography technique using electromagnetic waves. We demonstrate the capabilities of THz WART by imaging the cross sections of two test objects.

LETTER TO THE EDITOR: Constant-time solution to the global optimization problem using Brüschweiler's ensemble search algorithm

NASA Astrophysics Data System (ADS)

Protopopescu, V.; D'Helon, C.; Barhen, J.

2003-06-01

A constant-time solution of the continuous global optimization problem (GOP) is obtained by using an ensemble algorithm. We show that under certain assumptions, the solution can be guaranteed by mapping the GOP onto a discrete unsorted search problem, whereupon Brüschweiler's ensemble search algorithm is applied. For adequate sensitivities of the measurement technique, the query complexity of the ensemble search algorithm depends linearly on the size of the function's domain. Advantages and limitations of an eventual NMR implementation are discussed.

From lists of behaviour change techniques (BCTs) to structured hierarchies: comparison of two methods of developing a hierarchy of BCTs.

PubMed

Cane, James; Richardson, Michelle; Johnston, Marie; Ladha, Ruhina; Michie, Susan

2015-02-01

Behaviour change technique (BCT) Taxonomy v1 is a hierarchically grouped, consensus-based taxonomy of 93 BCTs for reporting intervention content. To enhance the use and understanding of BCTs, the aims of the present study were to (1) quantitatively examine the 'bottom-up' hierarchical structure of Taxonomy v1, (2) identify whether BCTs can be reliably mapped to theoretical domains using a 'top-down' theoretically driven approach, and (3) identify any overlap between the 'bottom-up' and 'top-down' groupings. The 'bottom-up' structure was examined for higher-order groupings using a dendrogram derived from hierarchical cluster analysis. For the theory-based 'top-down' structure, 18 experts sorted BCTs into 14 theoretical domains. Discriminant Content Validity was used to identify groupings, and chi-square tests and Pearson's residuals were used to examine the overlap between groupings. Behaviour change techniques relating to 'Reward and Punishment' and 'Cues and Cue Responses' were perceived as markedly different to other BCTs. Fifty-nine of the BCTs were reliably allocated to 12 of the 14 theoretical domains; 47 were significant and 12 were of borderline significance. Thirty-four of 208 'bottom-up' × 'top-down' pairings showed greater overlap than expected by chance. However, only six combinations achieved satisfactory evidence of similarity. The moderate overlap between the groupings indicates some tendency to implicitly conceptualize BCTs in terms of the same theoretical domains. Understanding the nature of the overlap will aid the conceptualization of BCTs in terms of theory and application. Further research into different methods of developing a hierarchical taxonomic structure of BCTs for international, interdisciplinary work is now required. Statement of contribution What is already known on this subject? Behaviour change interventions are effective in improving health care and health outcomes. The 'active' components of these interventions are behaviour change techniques and over 93 have been identified. Taxonomies of behaviour change techniques require structure to enable potential applications. What does this study add? This study identifies groups of BCTs to aid the recall of BCTs for intervention coding and design. It compares two methods of grouping--'bottom-up' and theory-based 'top-down'--and finds a moderate overlap. Building on identified BCT groups, it examines relationships between theoretical domains and BCTs. © 2014 The British Psychological Society.

Validating Domain Ontologies: A Methodology Exemplified for Concept Maps

ERIC Educational Resources Information Center

Steiner, Christina M.; Albert, Dietrich

2017-01-01

Ontologies play an important role as knowledge domain representations in technology-enhanced learning and instruction. Represented in form of concept maps they are commonly used as teaching and learning material and have the potential to enhance positive educational outcomes. To ensure the effective use of an ontology representing a knowledge…

Expert Concept Mapping Study on Mobile Learning

ERIC Educational Resources Information Center

Borner, Dirk; Glahn, Christian; Stoyanov, Slavi; Kalz, Marco; Specht, Marcus

2010-01-01

Purpose: The present paper introduces concept mapping as a structured participative conceptualization approach to identify clusters of ideas and opinions generated by experts within the domain of mobile learning. Utilizing this approach, the paper aims to contribute to a definition of key domain characteristics by identifying the main educational…

Mapping Social Interactions: The Science of Proxemics.

PubMed

McCall, Cade

Interpersonal distance and gaze provide a wealth of information during face-to-face social interactions. These "proxemic" behaviors offer a window into everyday social cognition by revealing interactants' affective states (e.g., interpersonal attitudes) and cognitive responses (e.g., social attention). Here we provide a brief overview of the social psychological literature in this domain. We focus on new techniques for experimentally manipulating and measuring proxemics, including the use of immersive virtual environments and digital motion capture. We also discuss ways in which these approaches can be integrated with psychophysiological and neuroimaging techniques. Throughout, we argue that contemporary proxemics research provides psychology and neuroscience with a means to study social cognition and behavior as they naturally emerge and unfold in vivo.

Meteor tracking via local pattern clustering in spatio-temporal domain

NASA Astrophysics Data System (ADS)

Kukal, Jaromír.; Klimt, Martin; Švihlík, Jan; Fliegel, Karel

2016-09-01

Reliable meteor detection is one of the crucial disciplines in astronomy. A variety of imaging systems is used for meteor path reconstruction. The traditional approach is based on analysis of 2D image sequences obtained from a double station video observation system. Precise localization of meteor path is difficult due to atmospheric turbulence and other factors causing spatio-temporal fluctuations of the image background. The proposed technique performs non-linear preprocessing of image intensity using Box-Cox transform as recommended in our previous work. Both symmetric and asymmetric spatio-temporal differences are designed to be robust in the statistical sense. Resulting local patterns are processed by data whitening technique and obtained vectors are classified via cluster analysis and Self-Organized Map (SOM).

On three-dimensional misorientation spaces.

PubMed

Krakow, Robert; Bennett, Robbie J; Johnstone, Duncan N; Vukmanovic, Zoja; Solano-Alvarez, Wilberth; Lainé, Steven J; Einsle, Joshua F; Midgley, Paul A; Rae, Catherine M F; Hielscher, Ralf

2017-10-01

Determining the local orientation of crystals in engineering and geological materials has become routine with the advent of modern crystallographic mapping techniques. These techniques enable many thousands of orientation measurements to be made, directing attention towards how such orientation data are best studied. Here, we provide a guide to the visualization of misorientation data in three-dimensional vector spaces, reduced by crystal symmetry, to reveal crystallographic orientation relationships. Domains for all point group symmetries are presented and an analysis methodology is developed and applied to identify crystallographic relationships, indicated by clusters in the misorientation space, in examples from materials science and geology. This analysis aids the determination of active deformation mechanisms and evaluation of cluster centres and spread enables more accurate description of transformation processes supporting arguments regarding provenance.

On three-dimensional misorientation spaces

NASA Astrophysics Data System (ADS)

Krakow, Robert; Bennett, Robbie J.; Johnstone, Duncan N.; Vukmanovic, Zoja; Solano-Alvarez, Wilberth; Lainé, Steven J.; Einsle, Joshua F.; Midgley, Paul A.; Rae, Catherine M. F.; Hielscher, Ralf

2017-10-01

Determining the local orientation of crystals in engineering and geological materials has become routine with the advent of modern crystallographic mapping techniques. These techniques enable many thousands of orientation measurements to be made, directing attention towards how such orientation data are best studied. Here, we provide a guide to the visualization of misorientation data in three-dimensional vector spaces, reduced by crystal symmetry, to reveal crystallographic orientation relationships. Domains for all point group symmetries are presented and an analysis methodology is developed and applied to identify crystallographic relationships, indicated by clusters in the misorientation space, in examples from materials science and geology. This analysis aids the determination of active deformation mechanisms and evaluation of cluster centres and spread enables more accurate description of transformation processes supporting arguments regarding provenance.

Hemichordates and the origin of chordates

NASA Technical Reports Server (NTRS)

Gerhart, John; Lowe, Christopher; Kirschner, Marc

2005-01-01

Hemichordates, the phylum of bilateral animals most closely related to chordates, could reveal the evolutionary origins of chordate traits such as the nerve cord, notochord, gill slits and tail. The anteroposterior maps of gene expression domains for 38 genes of chordate neural patterning are highly similar for hemichordates and chordates, even though hemichordates have a diffuse nerve-net. About 40% of the domains are not present in protostome maps. We propose that this map, the gill slits and the tail date to the deuterostome ancestor. The map of dorsoventral expression domains, centered on a Bmp-Chordin axis, differs between the two groups; hemichordates resemble protostomes more than they do chordates. The dorsoventral axis might have undergone extensive modification in the chordate line, including centralization of the nervous system, segregation of epidermis, derivation of the notochord, and an inversion of organization.

The synthesis map is a multidimensional educational tool that provides insight into students' mental models and promotes students' synthetic knowledge generation.

PubMed

Ortega, Ryan A; Brame, Cynthia J

2015-01-01

Concept mapping was developed as a method of displaying and organizing hierarchical knowledge structures. Using the new, multidimensional presentation software Prezi, we have developed a new teaching technique designed to engage higher-level skills in the cognitive domain. This tool, synthesis mapping, is a natural evolution of concept mapping, which utilizes embedding to layer information within concepts. Prezi's zooming user interface lets the author of the presentation use both depth as well as distance to show connections between data, ideas, and concepts. Students in the class Biology of Cancer created synthesis maps to illustrate their knowledge of tumorigenesis. Students used multiple organizational schemes to build their maps. We present an analysis of student work, placing special emphasis on organization within student maps and how the organization of knowledge structures in student maps can reveal strengths and weaknesses in student understanding or instruction. We also provide a discussion of best practices for instructors who would like to implement synthesis mapping in their classrooms. © 2015 R. A. Ortega and C. J. Brame et al. CBE—Life Sciences Education © 2015 The American Society for Cell Biology. This article is distributed by The American Society for Cell Biology under license from the author(s). It is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

Domain decomposition by the advancing-partition method for parallel unstructured grid generation

NASA Technical Reports Server (NTRS)

Banihashemi, legal representative, Soheila (Inventor); Pirzadeh, Shahyar Z. (Inventor)

2012-01-01

In a method for domain decomposition for generating unstructured grids, a surface mesh is generated for a spatial domain. A location of a partition plane dividing the domain into two sections is determined. Triangular faces on the surface mesh that intersect the partition plane are identified. A partition grid of tetrahedral cells, dividing the domain into two sub-domains, is generated using a marching process in which a front comprises only faces of new cells which intersect the partition plane. The partition grid is generated until no active faces remain on the front. Triangular faces on each side of the partition plane are collected into two separate subsets. Each subset of triangular faces is renumbered locally and a local/global mapping is created for each sub-domain. A volume grid is generated for each sub-domain. The partition grid and volume grids are then merged using the local-global mapping.

A unified approach for debugging is-a structure and mappings in networked taxonomies

PubMed Central

2013-01-01

Background With the increased use of ontologies and ontology mappings in semantically-enabled applications such as ontology-based search and data integration, the issue of detecting and repairing defects in ontologies and ontology mappings has become increasingly important. These defects can lead to wrong or incomplete results for the applications. Results We propose a unified framework for debugging the is-a structure of and mappings between taxonomies, the most used kind of ontologies. We present theory and algorithms as well as an implemented system RepOSE, that supports a domain expert in detecting and repairing missing and wrong is-a relations and mappings. We also discuss two experiments performed by domain experts: an experiment on the Anatomy ontologies from the Ontology Alignment Evaluation Initiative, and a debugging session for the Swedish National Food Agency. Conclusions Semantically-enabled applications need high quality ontologies and ontology mappings. One key aspect is the detection and removal of defects in the ontologies and ontology mappings. Our system RepOSE provides an environment that supports domain experts to deal with this issue. We have shown the usefulness of the approach in two experiments by detecting and repairing circa 200 and 30 defects, respectively. PMID:23548155

Characterization of Minerals of Geochronological Interest by EPMA and Atom Probe Tomography

NASA Astrophysics Data System (ADS)

Snoeyenbos, D.; Jercinovic, M. J.; Reinhard, D. A.; Hombourger, C.

2012-12-01

Isotopic and chemical dating techniques for zircon and monazite rely on several assumptions: that initial common Pb is low to nonexistent, that the analyzed domain is chronologically homogeneous, and that any relative migration of radiogenic Pb and its parent isotopes has not exceeded the analyzed domain. Yet, both zircon and monazite commonly contain significant submicron heterogeneities that may challenge these assumptions and can complicate the interpretation of chemical and isotopic data. Compositional mapping and submicron quantitative analysis by EPMA and FE-EPMA have been found to be useful techniques both for the characterization of these heterogeneities, and for quantitative geochronological determinations within the analytical limits of these techniques and the statistics of submicron sampling. Complementary to high-resolution EPMA techniques is Atom Probe Tomography (APT), wherein a specimen with dimensions of a few hundreds of nanometers is field evaporated atom by atom. The original position of each atom is identified, along with its atomic species and isotope. The result is a reconstruction allowing quantitative three-dimensional study of the specimen at the atomic scale, with low detection limits and high mass resolution. With the introduction of laser-induced thermal pulsing to achieve field evaporation, the technique is no longer limited to conductive specimens. There exists the capability to explore the compositional and isotopic structure of insulating materials at sub-nanometer resolution. Minerals of geochronological interest have been studied by an analytical method involving first compositional mapping and submicron quantitative analysis by EPMA and FE-EPMA, and subsequent use of these data to select specific sites for APT specimen extraction by FIB. Examples presented include 1) zircon from the Taconian of New England, USA, containing a fossil resorption front included between an unmodified igneous core, and a subsequent metamorphic overgrowth, with significant redistribution of U, Th, P and Y along microfracture arrays extending into the overgrowth, and 2) Paleoproterozoic monazite in thin bands <1μm wide along cleavage planes within much older (Neoarchean) monazite from the Boothia mainland of the Western Churchill Province, Canada.

Evaluation of geophysical techniques for the detection of paleochannels in the Oakland area of eastern Nebraska as part of the Eastern Nebraska Water Resource Assessment

USGS Publications Warehouse

Abraham, Jared D.; Bedrosian, Paul A.; Asch, Theodore H.; Ball, Lyndsay B.; Cannia, James C.; Phillips, Jeffery D.; Lackey, Susan

2012-01-01

Surface audio-magnetotelluric and time-domain electromagnetic methods achieved sufficient depth of penetration and indicated that the paleochannel was much more complex than the original geological model. Simulated and observed gravity anomalies indicate that imaging sand and gravel aquifers near Oakland, Nebraska, would be difficult due to the complex basement density contrasts. Interpretation of the magnetic data indicates no magnetic sources from geologic units above the bedrock surface. Based upon the analysis and interpretation of the four methods evaluated, we suggest a large-scale survey using a high-powered time-domain airborne system. This is the most efficient and cost-effective path forward for the Eastern Nebraska Water Assessment group to map paleochannels that lie beneath thick clay-rich glacial tills.

Mapping scientific frontiers : the quest for knowledge visualization.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Boyack, Kevin W.

Visualization of scientific frontiers is a relatively new field, yet it has a long history and many predecessors. The application of science to science itself has been undertaken for decades with notable early contributions by Derek Price, Thomas Kuhn, Diana Crane, Eugene Garfield, and many others. What is new is the field of information visualization and application of its techniques to help us understand the process of science in the making. In his new book, Chaomei Chen takes us on a journey through this history, touching on predecessors, and then leading us firmly into the new world of Mapping Scientificmore » Frontiers. Building on the foundation of his earlier book, Information Visualization and Virtual Environments, Chen's new offering is much less a tutorial in how to do information visualization, and much more a conceptual exploration of why and how the visualization of science can change the way we do science, amplified by real examples. Chen's stated intents for the book are: (1) to focus on principles of visual thinking that enable the identification of scientific frontiers; (2) to introduce a way to systematize the identification of scientific frontiers (or paradigms) through visualization techniques; and (3) to stimulate interdisciplinary research between information visualization and information science researchers. On all these counts, he succeeds. Chen's book can be broken into two parts which focus on the first two purposes stated above. The first, consisting of the initial four chapters, covers history and predecessors. Kuhn's theory of normal science punctuated by periods of revolution, now commonly known as paradigm shifts, motivates the work. Relevant predecessors outside the traditional field of information science such as cartography (both terrestrial and celestial), mapping the mind, and principles of visual association and communication, are given ample coverage. Chen also describes enabling techniques known to information scientists, such as multi-dimensional scaling, advanced dimensional reduction, social network analysis, Pathfinder network scaling, and landscape visualizations. No algorithms are given here; rather, these techniques are described from the point of view of enabling 'visual thinking'. The Generalized Similarity Analysis (GSA) technique used by Chen in his recent published papers is also introduced here. Information and computer science professionals would be wise not to skip through these early chapters. Although principles of gestalt psychology, cartography, thematic maps, and association techniques may be outside their technology comfort zone, or interest, these predecessors lay a groundwork for the 'visual thinking' that is required to create effective visualizations. Indeed, the great challenge in information visualization is to transform the abstract and intangible into something visible, concrete, and meaningful to the user. The second part of the book, covering the final three chapters, extends the mapping metaphor into the realm of scientific discovery through the structuring of literatures in a way that enables us to see scientific frontiers or paradigms. Case studies are used extensively to show the logical progression that has been made in recent years to get us to this point. Homage is paid to giants of the last 20 years including Michel Callon for co-word mapping, Henry Small for document co-citation analysis and specialty narratives (charting a path linking the different sciences), and Kate McCain for author co-citation analysis, whose work has led to the current state-of-the-art. The last two chapters finally answer the question - 'What does a scientific paradigm look like?' The visual answer given is specific to the GSA technique used by Chen, but does satisfy the intent of the book - to introduce a way to visually identify scientific frontiers. A variety of case studies, mostly from Chen's previously published work - supermassive black holes, cross-domain applications of Pathfinder networks, mass extinction debates, impact of Don Swanson's work, and mad cow disease and vCJD in humans - succeed in explaining how visualization can be used to show the development of, competition between, and eventual acceptance (or replacement) of scientific paradigms. Although not addressed specifically, Chen's work nonetheless makes the persuasive argument that visual maps alone are not sufficient to explain 'the making of science' to a non-expert in a particular field. Rather, expert knowledge is still required to interpret these maps and to explain the paradigms. This combination of visual maps and expert knowledge, used jointly to good effect in the book, becomes a potent means for explaining progress in science to the expert and non-expert alike. Work to extend the GSA technique to explore latent domain knowledge (important work that falls below the citation thresholds typically used in GSA) is also explored here.« less

The Integrated Taxonomy of Health Care: Classifying Both Complementary and Biomedical Practices Using a Uniform Classification Protocol

PubMed Central

Porcino, Antony; MacDougall, Colleen

2009-01-01

Background: Since the late 1980s, several taxonomies have been developed to help map and describe the interrelationships of complementary and alternative medicine (CAM) modalities. In these taxonomies, several issues are often incompletely addressed: A simple categorization process that clearly isolates a modality to a single conceptual categoryClear delineation of verticality—that is, a differentiation of scale being observed from individually applied techniques, through modalities (therapies), to whole medical systemsRecognition of CAM as part of the general field of health care Methods: Development of the Integrated Taxonomy of Health Care (ITHC) involved three stages: Development of a precise, uniform health glossaryAnalysis of the extant taxonomiesUse of an iterative process of classifying modalities and medical systems into categories until a failure to singularly classify a modality occurred, requiring a return to the glossary and adjustment of the classifying protocol Results: A full vertical taxonomy was developed that includes and clearly differentiates between techniques, modalities, domains (clusters of similar modalities), systems of health care (coordinated care system involving multiple modalities), and integrative health care. Domains are the classical primary focus of taxonomies. The ITHC has eleven domains: chemical/substance-based work, device-based work, soft tissue–focused manipulation, skeletal manipulation, fitness/movement instruction, mind–body integration/classical somatics work, mental/emotional–based work, bio-energy work based on physical manipulation, bio-energy modulation, spiritual-based work, unique assessments. Modalities are assigned to the domains based on the primary mode of interaction with the client, according the literature of the practitioners. Conclusions: The ITHC has several strengths: little interpretation is used while successfully assigning modalities to single domains; the issue of taxonomic verticality is fully resolved; and the design fully integrates the complementary health care fields of biomedicine and CAM. PMID:21589735

Wavelength resolved neutron transmission analysis to identify single crystal particles in historical metallurgy

NASA Astrophysics Data System (ADS)

Barzagli, E.; Grazzi, F.; Salvemini, F.; Scherillo, A.; Sato, H.; Shinohara, T.; Kamiyama, T.; Kiyanagi, Y.; Tremsin, A.; Zoppi, Marco

2014-07-01

The phase composition and the microstructure of four ferrous Japanese arrows of the Edo period (17th-19th century) has been determined through two complementary neutron techniques: Position-sensitive wavelength-resolved neutron transmission analysis (PS-WRNTA) and time-of-flight neutron diffraction (ToF-ND). Standard ToF-ND technique has been applied by using the INES diffractometer at the ISIS pulsed neutron source in the UK, while the innovative PS-WRNTA one has been performed at the J-PARC neutron source on the BL-10 NOBORU beam line using the high spatial high time resolution neutron imaging detector. With ToF-ND we were able to reach information about the quantitative distribution of the metal and non-metal phases, the texture level, the strain level and the domain size of each of the samples, which are important parameters to gain knowledge about the technological level of the Japanese weapon. Starting from this base of data, the more complex PS-WRNTA has been applied to the same samples. This experimental technique exploits the presence of the so-called Bragg edges, in the time-of-flight spectrum of neutrons transmitted through crystalline materials, to map the microstructural properties of samples. The two techniques are non-invasive and can be easily applied to archaeometry for an accurate microstructure mapping of metal and ceramic artifacts.

Minimum time search in uncertain dynamic domains with complex sensorial platforms.

PubMed

Lanillos, Pablo; Besada-Portas, Eva; Lopez-Orozco, Jose Antonio; de la Cruz, Jesus Manuel

2014-08-04

The minimum time search in uncertain domains is a searching task, which appears in real world problems such as natural disasters and sea rescue operations, where a target has to be found, as soon as possible, by a set of sensor-equipped searchers. The automation of this task, where the time to detect the target is critical, can be achieved by new probabilistic techniques that directly minimize the Expected Time (ET) to detect a dynamic target using the observation probability models and actual observations collected by the sensors on board the searchers. The selected technique, described in algorithmic form in this paper for completeness, has only been previously partially tested with an ideal binary detection model, in spite of being designed to deal with complex non-linear/non-differential sensorial models. This paper covers the gap, testing its performance and applicability over different searching tasks with searchers equipped with different complex sensors. The sensorial models under test vary from stepped detection probabilities to continuous/discontinuous differentiable/non-differentiable detection probabilities dependent on distance, orientation, and structured maps. The analysis of the simulated results of several static and dynamic scenarios performed in this paper validates the applicability of the technique with different types of sensor models.

Minimum Time Search in Uncertain Dynamic Domains with Complex Sensorial Platforms

PubMed Central

Lanillos, Pablo; Besada-Portas, Eva; Lopez-Orozco, Jose Antonio; de la Cruz, Jesus Manuel

2014-01-01

The minimum time search in uncertain domains is a searching task, which appears in real world problems such as natural disasters and sea rescue operations, where a target has to be found, as soon as possible, by a set of sensor-equipped searchers. The automation of this task, where the time to detect the target is critical, can be achieved by new probabilistic techniques that directly minimize the Expected Time (ET) to detect a dynamic target using the observation probability models and actual observations collected by the sensors on board the searchers. The selected technique, described in algorithmic form in this paper for completeness, has only been previously partially tested with an ideal binary detection model, in spite of being designed to deal with complex non-linear/non-differential sensorial models. This paper covers the gap, testing its performance and applicability over different searching tasks with searchers equipped with different complex sensors. The sensorial models under test vary from stepped detection probabilities to continuous/discontinuous differentiable/non-differentiable detection probabilities dependent on distance, orientation, and structured maps. The analysis of the simulated results of several static and dynamic scenarios performed in this paper validates the applicability of the technique with different types of sensor models. PMID:25093345

A joint estimation detection of Glaucoma progression in 3D spectral domain optical coherence tomography optic nerve head images

NASA Astrophysics Data System (ADS)

Belghith, Akram; Bowd, Christopher; Weinreb, Robert N.; Zangwill, Linda M.

2014-03-01

Glaucoma is an ocular disease characterized by distinctive changes in the optic nerve head (ONH) and visual field. Glaucoma can strike without symptoms and causes blindness if it remains without treatment. Therefore, early disease detection is important so that treatment can be initiated and blindness prevented. In this context, important advances in technology for non-invasive imaging of the eye have been made providing quantitative tools to measure structural changes in ONH topography, an essential element for glaucoma detection and monitoring. 3D spectral domain optical coherence tomography (SD-OCT), an optical imaging technique, has been commonly used to discriminate glaucomatous from healthy subjects. In this paper, we present a new framework for detection of glaucoma progression using 3D SD-OCT images. In contrast to previous works that the retinal nerve fiber layer (RNFL) thickness measurement provided by commercially available spectral-domain optical coherence tomograph, we consider the whole 3D volume for change detection. To integrate a priori knowledge and in particular the spatial voxel dependency in the change detection map, we propose the use of the Markov Random Field to handle a such dependency. To accommodate the presence of false positive detection, the estimated change detection map is then used to classify a 3D SDOCT image into the "non-progressing" and "progressing" glaucoma classes, based on a fuzzy logic classifier. We compared the diagnostic performance of the proposed framework to existing methods of progression detection.

A joint estimation detection of Glaucoma progression in 3D spectral domain optical coherence tomography optic nerve head images.

PubMed

Belghith, Akram; Bowd, Christopher; Weinreb, Robert N; Zangwill, Linda M

2014-03-18

Glaucoma is an ocular disease characterized by distinctive changes in the optic nerve head (ONH) and visual field. Glaucoma can strike without symptoms and causes blindness if it remains without treatment. Therefore, early disease detection is important so that treatment can be initiated and blindness prevented. In this context, important advances in technology for non-invasive imaging of the eye have been made providing quantitative tools to measure structural changes in ONH topography, an essential element for glaucoma detection and monitoring. 3D spectral domain optical coherence tomography (SD-OCT), an optical imaging technique, has been commonly used to discriminate glaucomatous from healthy subjects. In this paper, we present a new framework for detection of glaucoma progression using 3D SD-OCT images. In contrast to previous works that the retinal nerve fiber layer (RNFL) thickness measurement provided by commercially available spectral-domain optical coherence tomograph, we consider the whole 3D volume for change detection. To integrate a priori knowledge and in particular the spatial voxel dependency in the change detection map, we propose the use of the Markov Random Field to handle a such dependency. To accommodate the presence of false positive detection, the estimated change detection map is then used to classify a 3D SDOCT image into the "non-progressing" and "progressing" glaucoma classes, based on a fuzzy logic classifier. We compared the diagnostic performance of the proposed framework to existing methods of progression detection.

Knowledge Maps for E-Learning

ERIC Educational Resources Information Center

Lee, Jae Hwa; Segev, Aviv

2012-01-01

Maps such as concept maps and knowledge maps are often used as learning materials. These maps have nodes and links, nodes as key concepts and links as relationships between key concepts. From a map, the user can recognize the important concepts and the relationships between them. To build concept or knowledge maps, domain experts are needed.…

Multivariate statistical characterization of charged and uncharged domain walls in multiferroic hexagonal YMnO3 single crystal visualized by a spherical aberration-corrected STEM.

PubMed

Matsumoto, Takao; Ishikawa, Ryo; Tohei, Tetsuya; Kimura, Hideo; Yao, Qiwen; Zhao, Hongyang; Wang, Xiaolin; Chen, Dapeng; Cheng, Zhenxiang; Shibata, Naoya; Ikuhara, Yuichi

2013-10-09

A state-of-the-art spherical aberration-corrected STEM was fully utilized to directly visualize the multiferroic domain structure in a hexagonal YMnO3 single crystal at atomic scale. With the aid of multivariate statistical analysis (MSA), we obtained unbiased and quantitative maps of ferroelectric domain structures with atomic resolution. Such a statistical image analysis of the transition region between opposite polarizations has confirmed atomically sharp transitions of ferroelectric polarization both in antiparallel (uncharged) and tail-to-tail 180° (charged) domain boundaries. Through the analysis, a correlated subatomic image shift of Mn-O layers with that of Y layers, exhibiting a double-arc shape of reversed curvatures, have been elucidated. The amount of image shift in Mn-O layers along the c-axis is statistically significant as small as 0.016 nm, roughly one-third of the evident image shift of 0.048 nm in Y layers. Interestingly, a careful analysis has shown that such a subatomic image shift in Mn-O layers vanishes at the tail-to-tail 180° domain boundaries. Furthermore, taking advantage of the annular bright field (ABF) imaging technique combined with MSA, the tilting of MnO5 bipyramids, the very core mechanism of multiferroicity of the material, is evaluated.

Development of a behaviour change communication tool for medical students: the 'Tent Pegs' booklet.

PubMed

Chisholm, Anna; Hart, Jo; Mann, Karen; Peters, Sarah

2014-01-01

To describe the development and validation of a behaviour change communication tool for medical students. Behaviour change techniques (BCTs) were identified within the literature and used to inform a communication tool to support medical students in discussing health-related behaviour change with patients. BCTs were organized into an accessible format for medical students (the 'Tent Pegs' booklet) and validated using discriminant content validity methods with 11 expert judges. One-sample t-tests showed that judges reliably mapped BCTs onto six of the seven Tent Pegs domains (confidence rating means ranged from 4.0 to 5.1 out of 10, all p≤0.002). Only BCTs within the 'empowering people to change' domain were not significantly different from the value zero (mean confidence rating=1.2, p>0.05); these BCTs were most frequently allocated to the 'addressing thoughts and emotions' domain instead. BCTs within the Tent Pegs booklet are reliably allocated to corresponding behaviour change domains with the exception of those within the 'empowering people to change' domain. The existing evidence-base on BCTs can be used to directly inform development of a communication tool to support medical students facilitate health behaviour change with patients. Crown Copyright © 2013. Published by Elsevier Ireland Ltd. All rights reserved.

Shift and rotation invariant photorefractive crystal-based associative memory

NASA Astrophysics Data System (ADS)

Uang, Chii-Maw; Lin, Wei-Feng; Lu, Ming-Huei; Lu, Guowen; Lu, Mingzhe

1995-08-01

A shift and rotation invariant photorefractive (PR) crystal based associative memory is addressed. The proposed associative memory has three layers: the feature extraction, inner- product, and output mapping layers. The feature extraction is performed by expanding an input object into a set of circular harmonic expansions (CHE) in the Fourier domain to acquire both the shift and rotation invariant properties. The inner product operation is performed by taking the advantage of Bragg diffraction of the bulky PR-crystal. The output mapping is achieved by using the massive storage capacity of the PR-crystal. In the training process, memories are stored in another PR-crystal by using the wavelength multiplexing technique. During the recall process, the output from the winner-take-all processor decides which wavelength should be used to read out the memory from the PR-crystal.

Needlet estimation of cross-correlation between CMB lensing maps and LSS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bianchini, Federico; Renzi, Alessandro; Marinucci, Domenico, E-mail: fbianchini@sissa.it, E-mail: renzi@mat.uniroma2.it, E-mail: marinucc@mat.uniroma2.it

In this paper we develop a novel needlet-based estimator to investigate the cross-correlation between cosmic microwave background (CMB) lensing maps and large-scale structure (LSS) data. We compare this estimator with its harmonic counterpart and, in particular, we analyze the bias effects of different forms of masking. In order to address this bias, we also implement a MASTER-like technique in the needlet case. The resulting estimator turns out to have an extremely good signal-to-noise performance. Our analysis aims at expanding and optimizing the operating domains in CMB-LSS cross-correlation studies, similarly to CMB needlet data analysis. It is motivated especially by nextmore » generation experiments (such as Euclid) which will allow us to derive much tighter constraints on cosmological and astrophysical parameters through cross-correlation measurements between CMB and LSS.« less

Constraints Imposed by Rift Inheritance on the Compressional Reactivation of a Hyperextended Margin: Mapping Rift Domains in the North Iberian Margin and in the Cantabrian Mountains

NASA Astrophysics Data System (ADS)

Cadenas, P.; Fernández-Viejo, G.; Pulgar, J. A.; Tugend, J.; Manatschal, G.; Minshull, T. A.

2018-03-01

The Alpine Pyrenean-Cantabrian orogen developed along the plate boundary between Iberia and Europe, involving the inversion of Mesozoic hyperextended basins along the southern Biscay margin. Thus, this margin represents a natural laboratory to analyze the control of structural rift inheritance on the compressional reactivation of a continental margin. With the aim to identify former rift domains and investigate their role during the subsequent compression, we performed a structural analysis of the central and western North Iberian margin, based on the interpretation of seismic reflection profiles and local constraints from drill-hole data. Seismic interpretations and published seismic velocity models enabled the development of crustal thickness maps that helped to constrain further the offshore and onshore segmentation. Based on all these constraints, we present a rift domain map across the central and western North Iberian margin, as far as the adjacent western Cantabrian Mountains. Furthermore, we provide a first-order description of the margin segmentation resulting from its polyphase tectonic evolution. The most striking result is the presence of a hyperthinned domain (e.g., Asturian Basin) along the central continental platform that is bounded to the north by the Le Danois High, interpreted as a rift-related continental block separating two distinctive hyperextended domains. From the analysis of the rift domain map and the distribution of reactivation structures, we conclude that the landward limit of the necking domain and the hyperextended domains, respectively, guide and localize the compressional overprint. The Le Danois block acted as a local buttress, conditioning the inversion of the Asturian Basin.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wainwright, Haruko M.; Flores Orozco, Adrian; Bucker, Matthias

In floodplain environments, a naturally reduced zone (NRZ) is considered to be a common biogeochemical hot spot, having distinct microbial and geochemical characteristics. Although important for understanding their role in mediating floodplain biogeochemical processes, mapping the subsurface distribution of NRZs over the dimensions of a floodplain is challenging, as conventional wellbore data are typically spatially limited and the distribution of NRZs is heterogeneous. In this work, we present an innovative methodology for the probabilistic mapping of NRZs within a three-dimensional (3-D) subsurface domain using induced polarization imaging, which is a noninvasive geophysical technique. Measurements consist of surface geophysical surveys andmore » drilling-recovered sediments at the U.S. Department of Energy field site near Rifle, CO (USA). Inversion of surface time domain-induced polarization (TDIP) data yielded 3-D images of the complex electrical resistivity, in terms of magnitude and phase, which are associated with mineral precipitation and other lithological properties. By extracting the TDIP data values colocated with wellbore lithological logs, we found that the NRZs have a different distribution of resistivity and polarization from the other aquifer sediments. To estimate the spatial distribution of NRZs, we developed a Bayesian hierarchical model to integrate the geophysical and wellbore data. In addition, the resistivity images were used to estimate hydrostratigraphic interfaces under the floodplain. Validation results showed that the integration of electrical imaging and wellbore data using a Bayesian hierarchical model was capable of mapping spatially heterogeneous interfaces and NRZ distributions thereby providing a minimally invasive means to parameterize a hydrobiogeochemical model of the floodplain.« less

No elliptic islands for the universal area-preserving map

NASA Astrophysics Data System (ADS)

Johnson, Tomas

2011-07-01

A renormalization approach has been used in Eckmann et al (1982) and Eckmann et al (1984) to prove the existence of a universal area-preserving map, a map with hyperbolic orbits of all binary periods. The existence of a horseshoe, with positive Hausdorff dimension, in its domain was demonstrated in Gaidashev and Johnson (2009a). In this paper the coexistence problem is studied, and a computer-aided proof is given that no elliptic islands with period less than 18 exist in the domain. It is also shown that less than 1.5% of the measure of the domain consists of elliptic islands. This is proven by showing that the measure of initial conditions that escape to infinity is at least 98.5% of the measure of the domain, and we conjecture that the escaping set has full measure. This is highly unexpected, since generically it is believed that for conservative systems hyperbolicity and ellipticity coexist.

What is agenda setting in the clinical encounter? Consensus from literature review and expert consultation.

PubMed

Gobat, Nina; Kinnersley, Paul; Gregory, John W; Robling, Michael

2015-07-01

To establish consensus on the core domains of agenda setting in consultations. We reviewed the healthcare literature and, using a modified Delphi technique to embrace both patient and clinician perspectives, conducted an iterative online survey, with 30 experts in health communication. Participants described agenda setting and rated the importance of proposed domains. Consensus was determined where the group median was ≥5 on a 7-point Likert-like response scale, and the interquartile range fell to within one point on this scale. Relevant publications were identified in three overlapping bodies of healthcare literature. Survey respondents considered that agenda setting involved a process whereby patients and clinicians establish a joint focus for both their conversation and their working relationship. Consensus was obtained on six core domains: identifying patient talk topics, identifying clinician talk topics, agreement of shared priorities, establishing conversational focus, collaboration and engagement. New terminology--agenda mapping and agenda navigation--is proposed. We identified core agenda setting domains that embraced patient and clinician perspectives. An integrated conceptualization of agenda setting may now be used by researchers and educators in both clinician and patient focused interventions. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

AbsIDconvert: An absolute approach for converting genetic identifiers at different granularities

PubMed Central

2012-01-01

Background High-throughput molecular biology techniques yield vast amounts of data, often by detecting small portions of ribonucleotides corresponding to specific identifiers. Existing bioinformatic methodologies categorize and compare these elements using inferred descriptive annotation given this sequence information irrespective of the fact that it may not be representative of the identifier as a whole. Results All annotations, no matter the granularity, can be aligned to genomic sequences and therefore annotated by genomic intervals. We have developed AbsIDconvert, a methodology for converting between genomic identifiers by first mapping them onto a common universal coordinate system using an interval tree which is subsequently queried for overlapping identifiers. AbsIDconvert has many potential uses, including gene identifier conversion, identification of features within a genomic region, and cross-species comparisons. The utility is demonstrated in three case studies: 1) comparative genomic study mapping plasmodium gene sequences to corresponding human and mosquito transcriptional regions; 2) cross-species study of Incyte clone sequences; and 3) analysis of human Ensembl transcripts mapped by Affymetrix®; and Agilent microarray probes. AbsIDconvert currently supports ID conversion of 53 species for a given list of input identifiers, genomic sequence, or genome intervals. Conclusion AbsIDconvert provides an efficient and reliable mechanism for conversion between identifier domains of interest. The flexibility of this tool allows for custom definition identifier domains contingent upon the availability and determination of a genomic mapping interval. As the genomes and the sequences for genetic elements are further refined, this tool will become increasingly useful and accurate. AbsIDconvert is freely available as a web application or downloadable as a virtual machine at: http://bioinformatics.louisville.edu/abid/. PMID:22967011

Can single molecule localization microscopy be used to map closely spaced RGD nanodomains?

PubMed Central

Nicovich, Philip R.; Soeriyadi, Alexander; Nieves, Daniel J.; Gooding, J. Justin; Gaus, Katharina

2017-01-01

Cells sense and respond to nanoscale variations in the distribution of ligands to adhesion receptors. This makes single molecule localization microscopy (SMLM) an attractive tool to map the distribution of ligands on nanopatterned surfaces. We explore the use of SMLM spatial cluster analysis to detect nanodomains of the cell adhesion-stimulating tripeptide arginine-glycine-aspartic acid (RGD). These domains were formed by the phase separation of block copolymers with controllable spacing on the scale of tens of nanometers. We first determined the topology of the block copolymer with atomic force microscopy (AFM) and then imaged the localization of individual RGD peptides with direct stochastic optical reconstruction microscopy (dSTORM). To compare the data, we analyzed the dSTORM data with DBSCAN (density-based spatial clustering application with noise). The ligand distribution and polymer topology are not necessary identical since peptides may attach to the polymer outside the nanodomains and/or coupling and detection of peptides within the nanodomains is incomplete. We therefore performed simulations to explore the extent to which nanodomains could be mapped with dSTORM. We found that successful detection of nanodomains by dSTORM was influenced by the inter-domain spacing and the localization precision of individual fluorophores, and less by non-specific absorption of ligands to the substratum. For example, under our imaging conditions, DBSCAN identification of nanodomains spaced further than 50 nm apart was largely independent of background localisations, while nanodomains spaced closer than 50 nm required a localization precision of ~11 nm to correctly estimate the modal nearest neighbor distance (NDD) between nanodomains. We therefore conclude that SMLM is a promising technique to directly map the distribution and nanoscale organization of ligands and would benefit from an improved localization precision. PMID:28723958

A Quantitative Visual Mapping and Visualization Approach for Deep Ocean Floor Research

NASA Astrophysics Data System (ADS)

Hansteen, T. H.; Kwasnitschka, T.

2013-12-01

Geological fieldwork on the sea floor is still impaired by our inability to resolve features on a sub-meter scale resolution in a quantifiable reference frame and over an area large enough to reveal the context of local observations. In order to overcome these issues, we have developed an integrated workflow of visual mapping techniques leading to georeferenced data sets which we examine using state-of-the-art visualization technology to recreate an effective working style of field geology. We demonstrate a microbathymetrical workflow, which is based on photogrammetric reconstruction of ROV imagery referenced to the acoustic vehicle track. The advantage over established acoustical systems lies in the true three-dimensionality of the data as opposed to the perspective projection from above produced by downward looking mapping methods. A full color texture mosaic derived from the imagery allows studies at resolutions beyond the resolved geometry (usually one order of magnitude below the image resolution) while color gives additional clues, which can only be partly resolved in acoustic backscatter. The creation of a three-dimensional model changes the working style from the temporal domain of a video recording back to the spatial domain of a map. We examine these datasets using a custom developed immersive virtual visualization environment. The ARENA (Artificial Research Environment for Networked Analysis) features a (lower) hemispherical screen at a diameter of six meters, accommodating up to four scientists at once thus providing the ability to browse data interactively among a group of researchers. This environment facilitates (1) the development of spatial understanding analogue to on-land outcrop studies, (2) quantitative observations of seafloor morphology and physical parameters of its deposits, (3) more effective formulation and communication of working hypotheses.

Glaucoma diagnosis by mapping macula with Fourier domain optical coherence tomography

NASA Astrophysics Data System (ADS)

Tan, Ou; Lu, Ake; Chopra, Vik; Varma, Rohit; Hiroshi, Ishikawa; Schuman, Joel; Huang, David

2008-03-01

A new image segmentation method was developed to detect macular retinal sub-layers boundary on newly-developed Fourier-Domain Optical Coherence Tomography (FD-OCT) with macular grid scan pattern. The segmentation results were used to create thickness map of macular ganglion cell complex (GCC), which contains the ganglion cell dendrites, cell bodies and axons. Overall average and several pattern analysis parameters were defined on the GCC thickness map and compared for the diagnosis of glaucoma. Intraclass correlation (ICC) is used to compare the reproducibility of the parameters. Area under receiving operative characteristic curve (AROC) was calculated to compare the diagnostic power. The result is also compared to the output of clinical time-domain OCT (TD-OCT). We found that GCC based parameters had good repeatability and comparable diagnostic power with circumpapillary nerve fiber layer (cpNFL) thickness. Parameters based on pattern analysis can increase the diagnostic power of GCC macular mapping.

Functional implications of orientation maps in primary visual cortex

NASA Astrophysics Data System (ADS)

Koch, Erin; Jin, Jianzhong; Alonso, Jose M.; Zaidi, Qasim

2016-11-01

Stimulus orientation in the primary visual cortex of primates and carnivores is mapped as iso-orientation domains radiating from pinwheel centres, where orientation preferences of neighbouring cells change circularly. Whether this orientation map has a function is currently debated, because many mammals, such as rodents, do not have such maps. Here we show that two fundamental properties of visual cortical responses, contrast saturation and cross-orientation suppression, are stronger within cat iso-orientation domains than at pinwheel centres. These differences develop when excitation (not normalization) from neighbouring oriented neurons is applied to different cortical orientation domains and then balanced by inhibition from un-oriented neurons. The functions of the pinwheel mosaic emerge from these local intra-cortical computations: Narrower tuning, greater cross-orientation suppression and higher contrast gain of iso-orientation cells facilitate extraction of object contours from images, whereas broader tuning, greater linearity and less suppression of pinwheel cells generate selectivity for surface patterns and textures.

Genalogical approaches to ethical implications of informational assimilative integrated discovery systems (AIDS) in business

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pharhizgar, K.D.; Lunce, S.E.

1994-12-31

Development of knowledge-based technological acquisition techniques and customers` information profiles are known as assimilative integrated discovery systems (AIDS) in modern organizations. These systems have access through processing to both deep and broad domains of information in modern societies. Through these systems organizations and individuals can predict future trend probabilities and events concerning their customers. AIDSs are new techniques which produce new information which informants can use without the help of the knowledge sources because of the existence of highly sophisticated computerized networks. This paper has analyzed the danger and side effects of misuse of information through the illegal, unethical andmore » immoral access to the data-base in an integrated and assimilative information system as described above. Cognivistic mapping, pragmatistic informational design gathering, and holistic classifiable and distributive techniques are potentially abusive systems whose outputs can be easily misused by businesses when researching the firm`s customers.« less

FOLD-EM: automated fold recognition in medium- and low-resolution (4-15 Å) electron density maps.

PubMed

Saha, Mitul; Morais, Marc C

2012-12-15

Owing to the size and complexity of large multi-component biological assemblies, the most tractable approach to determining their atomic structure is often to fit high-resolution radiographic or nuclear magnetic resonance structures of isolated components into lower resolution electron density maps of the larger assembly obtained using cryo-electron microscopy (cryo-EM). This hybrid approach to structure determination requires that an atomic resolution structure of each component, or a suitable homolog, is available. If neither is available, then the amount of structural information regarding that component is limited by the resolution of the cryo-EM map. However, even if a suitable homolog cannot be identified using sequence analysis, a search for structural homologs should still be performed because structural homology often persists throughout evolution even when sequence homology is undetectable, As macromolecules can often be described as a collection of independently folded domains, one way of searching for structural homologs would be to systematically fit representative domain structures from a protein domain database into the medium/low resolution cryo-EM map and return the best fits. Taken together, the best fitting non-overlapping structures would constitute a 'mosaic' backbone model of the assembly that could aid map interpretation and illuminate biological function. Using the computational principles of the Scale-Invariant Feature Transform (SIFT), we have developed FOLD-EM-a computational tool that can identify folded macromolecular domains in medium to low resolution (4-15 Å) electron density maps and return a model of the constituent polypeptides in a fully automated fashion. As a by-product, FOLD-EM can also do flexible multi-domain fitting that may provide insight into conformational changes that occur in macromolecular assemblies.

The GAAIN Entity Mapper: An Active-Learning System for Medical Data Mapping.

PubMed

Ashish, Naveen; Dewan, Peehoo; Toga, Arthur W

2015-01-01

This work is focused on mapping biomedical datasets to a common representation, as an integral part of data harmonization for integrated biomedical data access and sharing. We present GEM, an intelligent software assistant for automated data mapping across different datasets or from a dataset to a common data model. The GEM system automates data mapping by providing precise suggestions for data element mappings. It leverages the detailed metadata about elements in associated dataset documentation such as data dictionaries that are typically available with biomedical datasets. It employs unsupervised text mining techniques to determine similarity between data elements and also employs machine-learning classifiers to identify element matches. It further provides an active-learning capability where the process of training the GEM system is optimized. Our experimental evaluations show that the GEM system provides highly accurate data mappings (over 90% accuracy) for real datasets of thousands of data elements each, in the Alzheimer's disease research domain. Further, the effort in training the system for new datasets is also optimized. We are currently employing the GEM system to map Alzheimer's disease datasets from around the globe into a common representation, as part of a global Alzheimer's disease integrated data sharing and analysis network called GAAIN. GEM achieves significantly higher data mapping accuracy for biomedical datasets compared to other state-of-the-art tools for database schema matching that have similar functionality. With the use of active-learning capabilities, the user effort in training the system is minimal.

The GAAIN Entity Mapper: An Active-Learning System for Medical Data Mapping

PubMed Central

Ashish, Naveen; Dewan, Peehoo; Toga, Arthur W.

2016-01-01

This work is focused on mapping biomedical datasets to a common representation, as an integral part of data harmonization for integrated biomedical data access and sharing. We present GEM, an intelligent software assistant for automated data mapping across different datasets or from a dataset to a common data model. The GEM system automates data mapping by providing precise suggestions for data element mappings. It leverages the detailed metadata about elements in associated dataset documentation such as data dictionaries that are typically available with biomedical datasets. It employs unsupervised text mining techniques to determine similarity between data elements and also employs machine-learning classifiers to identify element matches. It further provides an active-learning capability where the process of training the GEM system is optimized. Our experimental evaluations show that the GEM system provides highly accurate data mappings (over 90% accuracy) for real datasets of thousands of data elements each, in the Alzheimer's disease research domain. Further, the effort in training the system for new datasets is also optimized. We are currently employing the GEM system to map Alzheimer's disease datasets from around the globe into a common representation, as part of a global Alzheimer's disease integrated data sharing and analysis network called GAAIN1. GEM achieves significantly higher data mapping accuracy for biomedical datasets compared to other state-of-the-art tools for database schema matching that have similar functionality. With the use of active-learning capabilities, the user effort in training the system is minimal. PMID:26793094

Map as a Service: A Framework for Visualising and Maximising Information Return from Multi-Modal Wireless Sensor Networks

PubMed Central

Hammoudeh, Mohammad; Newman, Robert; Dennett, Christopher; Mount, Sarah; Aldabbas, Omar

2015-01-01

This paper presents a distributed information extraction and visualisation service, called the mapping service, for maximising information return from large-scale wireless sensor networks. Such a service would greatly simplify the production of higher-level, information-rich, representations suitable for informing other network services and the delivery of field information visualisations. The mapping service utilises a blend of inductive and deductive models to map sense data accurately using externally available knowledge. It utilises the special characteristics of the application domain to render visualisations in a map format that are a precise reflection of the concrete reality. This service is suitable for visualising an arbitrary number of sense modalities. It is capable of visualising from multiple independent types of the sense data to overcome the limitations of generating visualisations from a single type of sense modality. Furthermore, the mapping service responds dynamically to changes in the environmental conditions, which may affect the visualisation performance by continuously updating the application domain model in a distributed manner. Finally, a distributed self-adaptation function is proposed with the goal of saving more power and generating more accurate data visualisation. We conduct comprehensive experimentation to evaluate the performance of our mapping service and show that it achieves low communication overhead, produces maps of high fidelity, and further minimises the mapping predictive error dynamically through integrating the application domain model in the mapping service. PMID:26378539

Gravity domains and assembly of the North American continent by collisional tectonics

NASA Technical Reports Server (NTRS)

Thomas, M. D.; Grieve, R. A. F.; Sharpton, V. L.

1988-01-01

A gravity trend map of North America, based on a horizontal Bouguer gravity gradient map produced from gravity data for Canada and the conterminous United States, is presented and used to define a continental mosaic of gravity trend domains akin to structural domains. Contrasting trend characteristics at gravity domain boundaries support the concept of outward growth of the continent primarily by accretionary tectonics. Gravity patterns, however, indicate a different style of tectonics dominated in the development of now-buried Proterozoic orogenic belts in the south-central United States, supporting a view that these belts formed along the leading edge of a southward-migrating Proterozoic continental margin.

32 CFR 644.25 - Withdrawal of Public Domain for Defense Purposes.

Code of Federal Regulations, 2012 CFR

2012-07-01

... public domain land, water, or land and water, or restrictions on use of areas in the Continental Shelf, aggregating an area of more than 5,000 acres for any one defense project, shall be by Act of Congress. Upon... (annual rental) basis. (6) Map(s) indicating the exterior boundaries of the project; excepted areas, if...

32 CFR 644.25 - Withdrawal of Public Domain for Defense Purposes.

Code of Federal Regulations, 2011 CFR

2011-07-01

... public domain land, water, or land and water, or restrictions on use of areas in the Continental Shelf, aggregating an area of more than 5,000 acres for any one defense project, shall be by Act of Congress. Upon... (annual rental) basis. (6) Map(s) indicating the exterior boundaries of the project; excepted areas, if...

32 CFR 644.25 - Withdrawal of Public Domain for Defense Purposes.

Code of Federal Regulations, 2013 CFR

2013-07-01

... public domain land, water, or land and water, or restrictions on use of areas in the Continental Shelf, aggregating an area of more than 5,000 acres for any one defense project, shall be by Act of Congress. Upon... (annual rental) basis. (6) Map(s) indicating the exterior boundaries of the project; excepted areas, if...

32 CFR 644.25 - Withdrawal of Public Domain for Defense Purposes.

Code of Federal Regulations, 2010 CFR

2010-07-01

... public domain land, water, or land and water, or restrictions on use of areas in the Continental Shelf, aggregating an area of more than 5,000 acres for any one defense project, shall be by Act of Congress. Upon... (annual rental) basis. (6) Map(s) indicating the exterior boundaries of the project; excepted areas, if...

32 CFR 644.25 - Withdrawal of Public Domain for Defense Purposes.

Code of Federal Regulations, 2014 CFR

2014-07-01

... public domain land, water, or land and water, or restrictions on use of areas in the Continental Shelf, aggregating an area of more than 5,000 acres for any one defense project, shall be by Act of Congress. Upon... (annual rental) basis. (6) Map(s) indicating the exterior boundaries of the project; excepted areas, if...

Applicability of active infrared thermography for screening of human breast: a numerical study

NASA Astrophysics Data System (ADS)

Dua, Geetika; Mulaveesala, Ravibabu

2018-03-01

Active infrared thermography is a fast, painless, noncontact, and noninvasive imaging method, complementary to mammography, ultrasound, and magnetic resonance imaging methods for early diagnosis of breast cancer. This technique plays an important role in early detection of breast cancer to women of all ages, including pregnant or nursing women, with different sizes of breast, irrespective of either fatty or dense breast. This proposed complementary technique makes use of infrared emission emanating from the breast. Emanating radiations from the surface of the breast under test are detected with an infrared camera to map the thermal gradients over it, in order to reveal hidden tumors inside it. One of the reliable active infrared thermographic technique, linear frequency modulated thermal wave imaging is adopted to detect tumors present inside the breast. Further, phase and amplitude images are constructed using frequency and time-domain data analysis schemes. Obtained results show the potential of the proposed technique for early diagnosis of breast cancer in fatty as well as dense breasts.

Mapping edge-based traffic measurements onto the internal links in MPLS network

NASA Astrophysics Data System (ADS)

Zhao, Guofeng; Tang, Hong; Zhang, Yi

2004-09-01

Applying multi-protocol label switching techniques to IP-based backbone for traffic engineering goals has shown advantageous. Obtaining a volume of load on each internal link of the network is crucial for traffic engineering applying. Though collecting can be available for each link, such as applying traditional SNMP scheme, the approach may cause heavy processing load and sharply degrade the throughput of the core routers. Then monitoring merely at the edge of the network and mapping the measurements onto the core provides a good alternative way. In this paper, we explore a scheme for traffic mapping with edge-based measurements in MPLS network. It is supposed that the volume of traffic on each internal link over the domain would be mapped onto by measurements available only at ingress nodes. We apply path-based measurements at ingress nodes without enabling measurements in the core of the network. We propose a method that can infer a path from the ingress to the egress node using label distribution protocol without collecting routing data from core routers. Based on flow theory and queuing theory, we prove that our approach is effective and present the algorithm for traffic mapping. We also show performance simulation results that indicate potential of our approach.

A financial market model with two discontinuities: Bifurcation structures in the chaotic domain

NASA Astrophysics Data System (ADS)

Panchuk, Anastasiia; Sushko, Iryna; Westerhoff, Frank

2018-05-01

We continue the investigation of a one-dimensional piecewise linear map with two discontinuity points. Such a map may arise from a simple asset-pricing model with heterogeneous speculators, which can help us to explain the intricate bull and bear behavior of financial markets. Our focus is on bifurcation structures observed in the chaotic domain of the map's parameter space, which is associated with robust multiband chaotic attractors. Such structures, related to the map with two discontinuities, have been not studied before. We show that besides the standard bandcount adding and bandcount incrementing bifurcation structures, associated with two partitions, there exist peculiar bandcount adding and bandcount incrementing structures involving all three partitions. Moreover, the map's three partitions may generate intriguing bistability phenomena.

On three-dimensional misorientation spaces

PubMed Central

Bennett, Robbie J.; Vukmanovic, Zoja; Solano-Alvarez, Wilberth; Lainé, Steven J.; Einsle, Joshua F.; Midgley, Paul A.; Rae, Catherine M. F.; Hielscher, Ralf

2017-01-01

Determining the local orientation of crystals in engineering and geological materials has become routine with the advent of modern crystallographic mapping techniques. These techniques enable many thousands of orientation measurements to be made, directing attention towards how such orientation data are best studied. Here, we provide a guide to the visualization of misorientation data in three-dimensional vector spaces, reduced by crystal symmetry, to reveal crystallographic orientation relationships. Domains for all point group symmetries are presented and an analysis methodology is developed and applied to identify crystallographic relationships, indicated by clusters in the misorientation space, in examples from materials science and geology. This analysis aids the determination of active deformation mechanisms and evaluation of cluster centres and spread enables more accurate description of transformation processes supporting arguments regarding provenance. PMID:29118660

Functional interactions at the interface between voltage-sensing and pore domains in the Shaker K(v) channel.

PubMed

Soler-Llavina, Gilberto J; Chang, Tsg-Hui; Swartz, Kenton J

2006-11-22

Voltage-activated potassium (K(v)) channels contain a central pore domain that is partially surrounded by four voltage-sensing domains. Recent X-ray structures suggest that the two domains lack extensive protein-protein contacts within presumed transmembrane regions, but whether this is the case for functional channels embedded in lipid membranes remains to be tested. We investigated domain interactions in the Shaker K(v) channel by systematically mutating the pore domain and assessing tolerance by examining channel maturation, S4 gating charge movement, and channel opening. When mapped onto the X-ray structure of the K(v)1.2 channel the large number of permissive mutations support the notion of relatively independent domains, consistent with crystallographic studies. Inspection of the maps also identifies portions of the interface where residues are sensitive to mutation, an external cluster where mutations hinder voltage sensor activation, and an internal cluster where domain interactions between S4 and S5 helices from adjacent subunits appear crucial for the concerted opening transition.

Structural proteomics: Topology and relative accessibility of plant lipid droplet associated proteins.

PubMed

Jolivet, Pascale; Aymé, Laure; Giuliani, Alexandre; Wien, Frank; Chardot, Thierry; Gohon, Yann

2017-10-03

Lipid droplets are the major stock of lipids in oleaginous plant seeds. Despite their economic importance for oil production and biotechnological issues (biofuels, lubricants and plasticizers), numerous questions about their formation, structure and regulation are still unresolved. To determine water accessible domains of protein coating at lipid droplets surface, a structural proteomic approach has been performed. This technique relies on the millisecond timescale production of hydroxyl radicals by the radiolysis of water using Synchrotron X-ray white beam. Thanks to the evolution of mass spectrometry analysis techniques this approach allows the creation of a map of the solvent accessibility for proteins difficult to study by other means. Using these results, a S3 oleosin water accessibility map is proposed. This is the first time that such a map on an oleosin co-purified with plant lipid droplets and other associated protein is presented. Lipid droplet associated proteins function is linked to stability, structure and probably formation and lipid mobilization of droplets. Structure of these proteins in their native environment, at the interface between bulk water and the lipidic core of these organelles is only based on hydrophobicity plot. Using hydroxyl radical footprinting and proteomics approaches we studied water accessibility of one major protein in these droplets: S3 oleosin of Arabidopsis thaliana seeds. Copyright © 2017 Elsevier B.V. All rights reserved.

An Analogue VLSI Implementation of the Meddis Inner Hair Cell Model

NASA Astrophysics Data System (ADS)

McEwan, Alistair; van Schaik, André

2003-12-01

The Meddis inner hair cell model is a widely accepted, but computationally intensive computer model of mammalian inner hair cell function. We have produced an analogue VLSI implementation of this model that operates in real time in the current domain by using translinear and log-domain circuits. The circuit has been fabricated on a chip and tested against the Meddis model for (a) rate level functions for onset and steady-state response, (b) recovery after masking, (c) additivity, (d) two-component adaptation, (e) phase locking, (f) recovery of spontaneous activity, and (g) computational efficiency. The advantage of this circuit, over other electronic inner hair cell models, is its nearly exact implementation of the Meddis model which can be tuned to behave similarly to the biological inner hair cell. This has important implications on our ability to simulate the auditory system in real time. Furthermore, the technique of mapping a mathematical model of first-order differential equations to a circuit of log-domain filters allows us to implement real-time neuromorphic signal processors for a host of models using the same approach.

Pushing the limits of sulfur SAD phasing: de novo structure solution of the N-terminal domain of the ectodomain of HCV E1

DOE Office of Scientific and Technical Information (OSTI.GOV)

El Omari, Kamel; Iourin, Oleg; Kadlec, Jan

2014-08-01

The sulfur SAD phasing method was successfully used to determine the structure of the N-terminal domain of HCV E1 from low-resolution diffracting crystals by combining data from 32 crystals. Single-wavelength anomalous dispersion of S atoms (S-SAD) is an elegant phasing method to determine crystal structures that does not require heavy-atom incorporation or selenomethionine derivatization. Nevertheless, this technique has been limited by the paucity of the signal at the usual X-ray wavelengths, requiring very accurate measurement of the anomalous differences. Here, the data collection and structure solution of the N-terminal domain of the ectodomain of HCV E1 from crystals that diffractedmore » very weakly is reported. By combining the data from 32 crystals, it was possible to solve the sulfur substructure and calculate initial maps at 7 Å resolution, and after density modication and phase extension using a higher resolution native data set to 3.5 Å resolution model building was achievable.« less

Initial constructs for patient-centered outcome measures to evaluate brain-computer interfaces

PubMed Central

Andresen, Elena M.; Fried-Oken, Melanie; Peters, Betts; Patrick, Donald L.

2016-01-01

Purpose The authors describe preliminary work toward the creation of patient-centered outcome (PCO) measures to evaluate brain-computer interface (BCI) as an assistive technology for individuals with severe speech and physical impairments (SSPI). Method In Phase 1, 591 items from 15 existing measures were mapped to the International Classification of Functioning, Disability and Health (ICF). In Phase 2, qualitative interviews were conducted with eight people with SSPI and seven caregivers. Resulting text data were coded in an iterative analysis. Results Most items (79%) mapped to the ICF environmental domain; over half (53%) mapped to more than one domain. The ICF framework was well suited for mapping items related to body functions and structures, but less so for items in other areas, including personal factors. Two constructs emerged from qualitative data: Quality of Life (QOL) and Assistive Technology. Component domains and themes were identified for each. Conclusions Preliminary constructs, domains, and themes were generated for future PCO measures relevant to BCI. Existing instruments are sufficient for initial items but do not adequately match the values of people with SSPI and their caregivers. Field methods for interviewing people with SSPI were successful, and support the inclusion of these individuals in PCO research. PMID:25806719

Airborne electromagnetic bathymetry investigations in Port Lincoln, South Australia - comparison with an equivalent floating transient electromagnetic system

NASA Astrophysics Data System (ADS)

Vrbancich, Julian

2011-09-01

Helicopter time-domain airborne electromagnetic (AEM) methodology is being investigated as a reconnaissance technique for bathymetric mapping in shallow coastal waters, especially in areas affected by water turbidity where light detection and ranging (LIDAR) and hyperspectral techniques may be limited. Previous studies in Port Lincoln, South Australia, used a floating AEM time-domain system to provide an upper limit to the expected bathymetric accuracy based on current technology for AEM systems. The survey lines traced by the towed floating system were also flown with an airborne system using the same transmitter and receiver electronic instrumentation, on two separate occasions. On the second occasion, significant improvements had been made to the instrumentation to reduce the system self-response at early times. A comparison of the interpreted water depths obtained from the airborne and floating systems is presented, showing the degradation in bathymetric accuracy obtained from the airborne data. An empirical data correction method based on modelled and observed EM responses over deep seawater (i.e. a quasi half-space response) at varying survey altitudes, combined with known seawater conductivity measured during the survey, can lead to significant improvements in interpreted water depths and serves as a useful method for checking system calibration. Another empirical data correction method based on observed and modelled EM responses in shallow water was shown to lead to similar improvements in interpreted water depths; however, this procedure is notably inferior to the quasi half-space response because more parameters need to be assumed in order to compute the modelled EM response. A comparison between the results of the two airborne surveys in Port Lincoln shows that uncorrected data obtained from the second airborne survey gives good agreement with known water depths without the need to apply any empirical corrections to the data. This result significantly decreases the data-processing time thereby enabling the AEM method to serve as a rapid reconnaissance technique for bathymetric mapping.

A new multicriteria risk mapping approach based on a multiattribute frontier concept.

PubMed

Yemshanov, Denys; Koch, Frank H; Ben-Haim, Yakov; Downing, Marla; Sapio, Frank; Siltanen, Marty

2013-09-01

Invasive species risk maps provide broad guidance on where to allocate resources for pest monitoring and regulation, but they often present individual risk components (such as climatic suitability, host abundance, or introduction potential) as independent entities. These independent risk components are integrated using various multicriteria analysis techniques that typically require prior knowledge of the risk components' importance. Such information is often nonexistent for many invasive pests. This study proposes a new approach for building integrated risk maps using the principle of a multiattribute efficient frontier and analyzing the partial order of elements of a risk map as distributed in multidimensional criteria space. The integrated risks are estimated as subsequent multiattribute frontiers in dimensions of individual risk criteria. We demonstrate the approach with the example of Agrilus biguttatus Fabricius, a high-risk pest that may threaten North American oak forests in the near future. Drawing on U.S. and Canadian data, we compare the performance of the multiattribute ranking against a multicriteria linear weighted averaging technique in the presence of uncertainties, using the concept of robustness from info-gap decision theory. The results show major geographic hotspots where the consideration of tradeoffs between multiple risk components changes integrated risk rankings. Both methods delineate similar geographical regions of high and low risks. Overall, aggregation based on a delineation of multiattribute efficient frontiers can be a useful tool to prioritize risks for anticipated invasive pests, which usually have an extremely poor prior knowledge base. Published 2013. This article is a U.S. Government work and is in the public domain in the USA.

A strand graph semantics for DNA-based computation

PubMed Central

Petersen, Rasmus L.; Lakin, Matthew R.; Phillips, Andrew

2015-01-01

DNA nanotechnology is a promising approach for engineering computation at the nanoscale, with potential applications in biofabrication and intelligent nanomedicine. DNA strand displacement is a general strategy for implementing a broad range of nanoscale computations, including any computation that can be expressed as a chemical reaction network. Modelling and analysis of DNA strand displacement systems is an important part of the design process, prior to experimental realisation. As experimental techniques improve, it is important for modelling languages to keep pace with the complexity of structures that can be realised experimentally. In this paper we present a process calculus for modelling DNA strand displacement computations involving rich secondary structures, including DNA branches and loops. We prove that our calculus is also sufficiently expressive to model previous work on non-branching structures, and propose a mapping from our calculus to a canonical strand graph representation, in which vertices represent DNA strands, ordered sites represent domains, and edges between sites represent bonds between domains. We define interactions between strands by means of strand graph rewriting, and prove the correspondence between the process calculus and strand graph behaviours. Finally, we propose a mapping from strand graphs to an efficient implementation, which we use to perform modelling and simulation of DNA strand displacement systems with rich secondary structure. PMID:27293306

Predicting PDZ domain mediated protein interactions from structure

PubMed Central

2013-01-01

Background PDZ domains are structural protein domains that recognize simple linear amino acid motifs, often at protein C-termini, and mediate protein-protein interactions (PPIs) in important biological processes, such as ion channel regulation, cell polarity and neural development. PDZ domain-peptide interaction predictors have been developed based on domain and peptide sequence information. Since domain structure is known to influence binding specificity, we hypothesized that structural information could be used to predict new interactions compared to sequence-based predictors. Results We developed a novel computational predictor of PDZ domain and C-terminal peptide interactions using a support vector machine trained with PDZ domain structure and peptide sequence information. Performance was estimated using extensive cross validation testing. We used the structure-based predictor to scan the human proteome for ligands of 218 PDZ domains and show that the predictions correspond to known PDZ domain-peptide interactions and PPIs in curated databases. The structure-based predictor is complementary to the sequence-based predictor, finding unique known and novel PPIs, and is less dependent on training–testing domain sequence similarity. We used a functional enrichment analysis of our hits to create a predicted map of PDZ domain biology. This map highlights PDZ domain involvement in diverse biological processes, some only found by the structure-based predictor. Based on this analysis, we predict novel PDZ domain involvement in xenobiotic metabolism and suggest new interactions for other processes including wound healing and Wnt signalling. Conclusions We built a structure-based predictor of PDZ domain-peptide interactions, which can be used to scan C-terminal proteomes for PDZ interactions. We also show that the structure-based predictor finds many known PDZ mediated PPIs in human that were not found by our previous sequence-based predictor and is less dependent on training–testing domain sequence similarity. Using both predictors, we defined a functional map of human PDZ domain biology and predict novel PDZ domain function. Users may access our structure-based and previous sequence-based predictors at http://webservice.baderlab.org/domains/POW. PMID:23336252

Porcine MAP3K5 analysis: molecular cloning, characterization, tissue expression pattern, and copy number variations associated with residual feed intake.

PubMed

Pu, L; Zhang, L C; Zhang, J S; Song, X; Wang, L G; Liang, J; Zhang, Y B; Liu, X; Yan, H; Zhang, T; Yue, J W; Li, N; Wu, Q Q; Wang, L X

2016-08-12

Mitogen-activated protein kinase kinase kinase 5 (MAP3K5) is essential for apoptosis, proliferation, differentiation, and immune responses, and is a candidate marker for residual feed intake (RFI) in pig. We cloned the full-length cDNA sequence of porcine MAP3K5 by rapid-amplification of cDNA ends. The 5451-bp gene contains a 5'-untranslated region (UTR) (718 bp), a coding region (3738 bp), and a 3'-UTR (995 bp), and encodes a peptide of 1245 amino acids, which shares 97, 99, 97, 93, 91, and 84% sequence identity with cattle, sheep, human, mouse, chicken, and zebrafish MAP3K5, respectively. The deduced MAP3K5 protein sequence contains two conserved domains: a DUF4071 domain and a protein kinase domain. Phylogenetic analysis showed that porcine MAP3K5 forms a separate branch to vicugna and camel MAP3K5. Tissue expression analysis using real-time quantitative polymerase chain reaction (qRT-PCR) revealed that MAP3K5 was expressed in the heart, liver, spleen, lung, kidney, muscle, fat, pancrea, ileum, and stomach tissues. Copy number variation was detected for porcine MAP3K5 and validated by qRT-PCR. Furthermore, a significant increase in average copy number was detected in the low RFI group when compared to the high RFI group in a Duroc pig population. These results provide useful information regarding the influence of MAP3K5 on RFI in pigs.

Linking late cognitive outcome with glioma surgery location using resection cavity maps.

PubMed

Hendriks, Eef J; Habets, Esther J J; Taphoorn, Martin J B; Douw, Linda; Zwinderman, Aeilko H; Vandertop, W Peter; Barkhof, Frederik; Klein, Martin; De Witt Hamer, Philip C

2018-05-01

Patients with a diffuse glioma may experience cognitive decline or improvement upon resective surgery. To examine the impact of glioma location, cognitive alteration after glioma surgery was quantified and related to voxel-based resection probability maps. A total of 59 consecutive patients (range 18-67 years of age) who had resective surgery between 2006 and 2011 for a supratentorial nonenhancing diffuse glioma (grade I-III, WHO 2007) were included in this observational cohort study. Standardized neuropsychological examination and MRI were obtained before and after surgery. Intraoperative stimulation mapping guided resections towards neurological functions (language, sensorimotor function, and visual fields). Maps of resected regions were constructed in standard space. These resection cavity maps were compared between patients with and without new cognitive deficits (z-score difference >1.5 SD between baseline and one year after resection), using a voxel-wise randomization test and calculation of false discovery rates. Brain regions significantly associated with cognitive decline were classified in standard cortical and subcortical anatomy. Cognitive improvement in any domain occurred in 10 (17%) patients, cognitive decline in any domain in 25 (42%), and decline in more than one domain in 10 (17%). The most frequently affected subdomains were attention in 10 (17%) patients and information processing speed in 9 (15%). Resection regions associated with decline in more than one domain were predominantly located in the right hemisphere. For attention decline, no specific region could be identified. For decline in information speed, several regions were found, including the frontal pole and the corpus callosum. Cognitive decline after resective surgery of diffuse glioma is prevalent, in particular, in patients with a tumor located in the right hemisphere without cognitive function mapping. © The Authors Human Brain Mapping Published by Wiley Periodicals, Inc.

Determining the Exchangeability of Concept Map and Problem-Solving Essay Scores

ERIC Educational Resources Information Center

Hollenbeck, Keith; Twyman, Todd; Tindal, Gerald

2006-01-01

This study investigated the score exchangeability of concept maps with problem-solving essays. Of interest was whether sixth-grade students' concept maps predicted their scores on essay responses that used concept map content. Concept maps were hypothesized to be alternatives to performance assessments for content-area domain knowledge in science.…

Reynolds stress closure in jet flows using wave models

NASA Technical Reports Server (NTRS)

Morris, Philip J.

1990-01-01

A collection of papers is presented. The outline of this report is as follows. Chapter three contains a description of a weakly nonlinear turbulence model that was developed. An essential part of the application of such a closure scheme to general geometry jets is the solution of the local hydrodynamic stability equation for a given jet cross-section. Chapter four describes the conformal mapping schemes used to map such geometries onto a simple computational domain. Chapter five describes a solution of a stability problem for circular, elliptic, and rectangular geometries. In chapter six linear models for the shock shell structure in non-circular jets is given. The appendices contain reprints of papers also published during this study including the following topics: (1) instability of elliptic jets; (2) a technique for predicting the shock cell structure in non-circular jets using a vortex sheet model; and (3) the resonant interaction between twin supersonic jets.

The new and computationally efficient MIL-SOM algorithm: potential benefits for visualization and analysis of a large-scale high-dimensional clinically acquired geographic data.

PubMed

Oyana, Tonny J; Achenie, Luke E K; Heo, Joon

2012-01-01

The objective of this paper is to introduce an efficient algorithm, namely, the mathematically improved learning-self organizing map (MIL-SOM) algorithm, which speeds up the self-organizing map (SOM) training process. In the proposed MIL-SOM algorithm, the weights of Kohonen's SOM are based on the proportional-integral-derivative (PID) controller. Thus, in a typical SOM learning setting, this improvement translates to faster convergence. The basic idea is primarily motivated by the urgent need to develop algorithms with the competence to converge faster and more efficiently than conventional techniques. The MIL-SOM algorithm is tested on four training geographic datasets representing biomedical and disease informatics application domains. Experimental results show that the MIL-SOM algorithm provides a competitive, better updating procedure and performance, good robustness, and it runs faster than Kohonen's SOM.

The New and Computationally Efficient MIL-SOM Algorithm: Potential Benefits for Visualization and Analysis of a Large-Scale High-Dimensional Clinically Acquired Geographic Data

PubMed Central

Oyana, Tonny J.; Achenie, Luke E. K.; Heo, Joon

2012-01-01

The objective of this paper is to introduce an efficient algorithm, namely, the mathematically improved learning-self organizing map (MIL-SOM) algorithm, which speeds up the self-organizing map (SOM) training process. In the proposed MIL-SOM algorithm, the weights of Kohonen's SOM are based on the proportional-integral-derivative (PID) controller. Thus, in a typical SOM learning setting, this improvement translates to faster convergence. The basic idea is primarily motivated by the urgent need to develop algorithms with the competence to converge faster and more efficiently than conventional techniques. The MIL-SOM algorithm is tested on four training geographic datasets representing biomedical and disease informatics application domains. Experimental results show that the MIL-SOM algorithm provides a competitive, better updating procedure and performance, good robustness, and it runs faster than Kohonen's SOM. PMID:22481977

Sub-Domains of Ricin’s B Subunit as Targets of Toxin Neutralizing and Non-Neutralizing Monoclonal Antibodies

PubMed Central

Yermakova, Anastasiya; Vance, David J.; Mantis, Nicholas J.

2012-01-01

The B subunit (RTB) of ricin toxin is a galactose (Gal)−/N-acetylgalactosamine (GalNac)-specific lectin that mediates attachment, entry, and intracellular trafficking of ricin in host cells. Structurally, RTB consists of two globular domains with identical folding topologies. Domains 1 and 2 are each comprised of three homologous sub-domains (α, β, γ) that likely arose by gene duplication from a primordial carbohydrate recognition domain (CRD), although only sub-domains 1α and 2γ retain functional lectin activity. As part of our ongoing effort to generate a comprehensive B cell epitope map of ricin, we report the characterization of three new RTB-specific monoclonal antibodies (mAbs). All three mAbs, JB4, B/J F9 and C/M A2, were initially identified based on their abilities to neutralize ricin in a Vero cell cytotoxicty assay and to partially (or completely) block ricin attachment to cell surfaces. However, only JB4 proved capable of neutralizing ricin in a macrophage apoptosis assay and in imparting passive immunity to mice in a model of systemic intoxication. Using a combination of techniques, including competitive ELISAs, pepscan analysis, differential reactivity by Western blot, as well as affinity enrichment of phage displayed peptides, we tentatively localized the epitopes recognized by the non-neutralizing mAbs B/J F9 and C/M A2 to sub-domains 2α and 2β, respectively. Furthermore, we propose that the epitope recognized by JB4 is within sub-domain 2γ, adjacent to RTB’s high affinity Gal/GalNAc CRD. These data suggest that recognition of RTB’s sub-domains 1α and 2γ are critical determinants of antibody neutralizing activity and protective immunity to ricin. PMID:22984492

Hot deformation characteristics of INCONEL alloy MA 754 and development of a processing map

DOE Office of Scientific and Technical Information (OSTI.GOV)

Somani, M.C.; Muraleedharan, K.; Birla, N.C.

1994-08-01

The characteristics of hot deformation of INCONEL alloy MA 754 have been studies using processing maps obtained on the basis of flow stress data generated in compression in the temperature range 700 C to 1,150 C and strain rate range 0.001 to 100 s[sup [minus]1]. The map exhibited three domains. (1) A domain of dynamic recovery occurs in the temperature range 800 C to 1,075 C and strain rate range 0.02 to 2 s[sup [minus]1], with a peak efficiency of 18 pct occurring at 950 C and 0.1 s [sup [minus]1]. Transmission electron microscope (TEM) micrographs revealed stable subgrain structuremore » in this domain with the subgrain size increasing exponentially with an increase in temperature. (2) A domain exhibiting grain boundary cracking occurs at temperatures lower than 800 C and strain rates lower than 0.01 s[sup [minus]1]. (3) A domain exhibiting intense grain boundary cavitation occurs at temperatures higher than 1075 C. The material did not exhibit a dynamic recrystallization (DRX) domain, unlike other superalloys. At strain rates higher than about 1 s[sup [minus]1], the material exhibits flow instabilities manifesting as kinking of the elongated grains and adiabatic shear bands. The materials may be safely worked in the domain of dynamic recovery but can only be statically recrystallized.« less

On the influence of ocean waves on simulated GNSS-R delay-doppler maps

NASA Astrophysics Data System (ADS)

Clarizia, M. P.; di Bisceglie, M.; Galdi, C.; Gommenginger, C.; Srokosz, M.

2012-04-01

Global Navigation Satellite System-Reflectometry (GNSS-R), is an established technique that exploits GNSS signals of opportunity reflected from the surface of the ocean, to look primarily at the ocean surface roughness. The strength of this technique, and the primary motivation to carry it forward, is in the fact that GNSS signals are available globally, all the time and over the long term, and could help dramatically improve the monitoring of ocean wind and waves. GNSS-R offers the prospect of high density global measurements of directional sea surface roughness, which are essential for scientific purposes (i.e. quantifying the air-sea exchanges of gases), operational weather and ocean forecasting (i.e. prediction of high winds, dangerous sea states, risk of flooding and storm surges) and to support important climate-relevant Earth Observation techniques (IR SST, or surface salinity retrieval). The retrieval of ocean roughness from GNSS-R data has now been demonstrated with a reasonable level of accuracy from both airborne [1] and spaceborne [2] platforms. In both cases, Directional Mean Square Slopes (DMSS) of the ocean surface have been retrieved from GNSS-R data, in the form of Delay-Doppler Maps (DDMs), using an established theoretical scattering model by Zavorotny and Voronovich (Z-V) [3]. The need for a better assessment of the way the ocean waves influence the scattering of GPS signals has recently led to a different approach, consisting of simulating the scattering of such signals, using a more sophisticated large-scale scattering model than Z-V, and explicit simulations of realistic seas. Initial results produced from these simulations have been recently published in [4], where the emphasis has been put on the effects of different sea states on Radar Cross Section (RCS) and Polarization Ratio (PR) in space domain. Linear wind wave surfaces have been simulated using the Elfouhaily wind wave spectrum [5], for different wind speeds and directions, and with or without a superimposed swell. Then, the scattering from such surfaces has been computed using the innovative Facet Approach (FA), which approximates the surface through a number of rectangular facets, differently oriented, and calculates the surface scattering as the ensemble of the signals scattered from all the facets. Here we proceed with the next step of the GPS-Reflectometry simulator, through investigation of the results in Delay- Doppler (DD) domain. Changes and variations of the DDMs, computed using the FA scattering model, are investigated for a variety of wind and wave conditions of the underlying sea surfaces simulated. Results are analysed for changing wind speed and direction of the waves, presence of a swell component superimposed on wind waves, and changing parameters (wavelength, amplitude, direction) of the swell, revealing some degree of sensitivity of these maps to different sea states. The effect of polarization is also taken into account, through an analysis of PR in DD domain. Finally, an initial investigation into the effect of nonlinearities on the sea surface in DD domain is carried out, by looking at DDMs of the signal scattered from non linear non gaussian sea surfaces explicitly simulated.

A Mapping of the Electron Localization Function for Earth Materials

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gibbs, Gerald V.; Cox, David F.; Ross, Nancy

2005-06-01

The electron localization function, ELF, generated for a number of geometry-optimized earth materials, provides a graphical representation of the spatial localization of the probability electron density distribution as embodied in domains ascribed to localized bond and lone pair electrons. The lone pair domains, displayed by the silica polymorphs quartz, coesite and cristobalite, are typically banana-shaped and oriented perpendicular to the plane of the SiOSi angle at ~0.60 Å from the O atom on the reflex side of the angle. With decreasing angle, the domains increase in magnitude, indicating an increase in the nucleophilic character of the O atom, rendering itmore » more susceptible to potential electrophilic attack. The Laplacian isosurface maps of the experimental and theoretical electron density distribution for coesite substantiates the increase in the size of the domain with decreasing angle. Bond pair domains are displayed along each of the SiO bond vectors as discrete concave hemispherically-shaped domains at ~0.70 Å from the O atom. For more closed-shell ionic bonded interactions, the bond and lone pair domains are often coalesced, resulting in concave hemispherical toroidal-shaped domains with local maxima centered along the bond vectors. As the shared covalent character of the bonded interactions increases, the bond and lone pair domains are better developed as discrete domains. ELF isosurface maps generated for the earth materials tremolite, diopside, talc and dickite display banana-shaped lone pair domains associated with the bridging O atoms of SiOSi angles and concave hemispherical toroidal bond pair domains associated with the nonbridging ones. The lone pair domains in dickite and talc provide a basis for understanding the bonded interactions between the adjacent neutral layers. Maps were also generated for beryl, cordierite, quartz, low albite, forsterite, wadeite, åkermanite, pectolite, periclase, hurlbutite, thortveitite and vanthoffite. Strategies are reviewed for finding potential H docking sites in the silica polymorphs and related materials. As observed in an earlier study, the ELF is capable of generating bond and lone pair domains that are similar in number and arrangement to those provided by Laplacian and deformation electron density distributions. The formation of the bond and lone pair domains in the silica polymorphs and the progressive decrease in the SiO length as the value of the electron density at the bond critical point increases indicates that the SiO bonded interaction has a substantial component of covalent character.« less

Magnetometry of single ferromagnetic nanoparticles using magneto-optical indicator films with spatial amplification

DOE Office of Scientific and Technical Information (OSTI.GOV)

Balk, Andrew L., E-mail: andrew.balk@nist.gov; Maryland NanoCenter, University of Maryland, College Park, Maryland 20742; Hangarter, Carlos

2015-03-16

We present a magneto-optical technique to spatially amplify and image fringe fields from single ferromagnetic nanorods. The fringe fields nucleate magnetic domains in a low-coercivity, perpendicularly magnetized indicator film, which are expanded by an applied out-of-plane field from the nanoscale to the microscale for measurement with polar Kerr microscopy. The nucleation location and therefore magnetic orientation of the sample nanorod are detected as spatially dependent field biases in locally measured hysteresis loops of the indicator film. We first discuss our method to fabricate the high-sensitivity indicator film with low energy argon ion irradiation. We then present a map of themore » amplified signal produced from a single nanorod as measured by the indicator film and compare it with a simultaneously obtained, unamplified fringe field map. The comparison demonstrates the advantage of the amplification mechanism and the capability of the technique to be performed with single-spot magneto-optical Kerr effect magnetometers. Our signal-to-noise ratio determines a minimum measureable particle diameter of tens of nanometers for typical transition metals. We finally use our method to obtain hysteresis loops from multiple nanorods in parallel. Our technique is unperturbed by applied in-plane fields for magnetic manipulation of nanoparticles, is robust against many common noise sources, and is applicable in a variety of test environments. We conclude with a discussion of the future optimization and application of our indicator film technique.« less

Geologic applications of thermal-inertia mapping from satellite. [Powder River, Wyoming; Cubeza Prieta, Arizona, and Yellowstone National Park

NASA Technical Reports Server (NTRS)

Offield, T. W. (Principal Investigator); Watson, K.; Hummer-Miller, S.

1981-01-01

In the Powder River Basin, Wyo., narrow geologic units having thermal inertias which contrast with their surroundings can be discriminated in optimal images. A few subtle thermal inertia anomalies coincide with areas of helium leakage believed to be associated with deep oil and gas concentrations. The most important results involved delineation of tectonic framework elements some of which were not previously recognized. Thermal and thermal inertia images also permit mapping of geomorphic textural domains. A thermal lineament appears to reveal a basement discontinuity which involves the Homestake Mine in the Black Hill, a zone of Tertiary igneous activity and facies control in oil producing horizons. Applications of these data to the Cabeza Prieta, Ariz., area illustrate their potential for igneous rock type discrimination. Extension to Yellowstone National Park resulted in the detection of additional structural information but surface hydrothermal features could not be distinguished with any confidence. A thermal inertia mapping algorithm, a fast and accurate image registration technique, and an efficient topographic slope and elevation correction method were developed.

Autonomous mental development with selective attention, object perception, and knowledge representation

NASA Astrophysics Data System (ADS)

Ban, Sang-Woo; Lee, Minho

2008-04-01

Knowledge-based clustering and autonomous mental development remains a high priority research topic, among which the learning techniques of neural networks are used to achieve optimal performance. In this paper, we present a new framework that can automatically generate a relevance map from sensory data that can represent knowledge regarding objects and infer new knowledge about novel objects. The proposed model is based on understating of the visual what pathway in our brain. A stereo saliency map model can selectively decide salient object areas by additionally considering local symmetry feature. The incremental object perception model makes clusters for the construction of an ontology map in the color and form domains in order to perceive an arbitrary object, which is implemented by the growing fuzzy topology adaptive resonant theory (GFTART) network. Log-polar transformed color and form features for a selected object are used as inputs of the GFTART. The clustered information is relevant to describe specific objects, and the proposed model can automatically infer an unknown object by using the learned information. Experimental results with real data have demonstrated the validity of this approach.

Prediction of heterotrimeric protein complexes by two-phase learning using neighboring kernels

PubMed Central

2014-01-01

Background Protein complexes play important roles in biological systems such as gene regulatory networks and metabolic pathways. Most methods for predicting protein complexes try to find protein complexes with size more than three. It, however, is known that protein complexes with smaller sizes occupy a large part of whole complexes for several species. In our previous work, we developed a method with several feature space mappings and the domain composition kernel for prediction of heterodimeric protein complexes, which outperforms existing methods. Results We propose methods for prediction of heterotrimeric protein complexes by extending techniques in the previous work on the basis of the idea that most heterotrimeric protein complexes are not likely to share the same protein with each other. We make use of the discriminant function in support vector machines (SVMs), and design novel feature space mappings for the second phase. As the second classifier, we examine SVMs and relevance vector machines (RVMs). We perform 10-fold cross-validation computational experiments. The results suggest that our proposed two-phase methods and SVM with the extended features outperform the existing method NWE, which was reported to outperform other existing methods such as MCL, MCODE, DPClus, CMC, COACH, RRW, and PPSampler for prediction of heterotrimeric protein complexes. Conclusions We propose two-phase prediction methods with the extended features, the domain composition kernel, SVMs and RVMs. The two-phase method with the extended features and the domain composition kernel using SVM as the second classifier is particularly useful for prediction of heterotrimeric protein complexes. PMID:24564744

A general framework of TOPSIS method for integration of airborne geophysics, satellite imagery, geochemical and geological data

NASA Astrophysics Data System (ADS)

Abedi, Maysam; Norouzi, Gholam-Hossain

2016-04-01

This work presents the promising application of three variants of TOPSIS method (namely the conventional, adjusted and modified versions) as a straightforward knowledge-driven technique in multi criteria decision making processes for data fusion of a broad exploratory geo-dataset in mineral potential/prospectivity mapping. The method is implemented to airborne geophysical data (e.g. potassium radiometry, aeromagnetic and frequency domain electromagnetic data), surface geological layers (fault and host rock zones), extracted alteration layers from remote sensing satellite imagery data, and five evidential attributes from stream sediment geochemical data. The central Iranian volcanic-sedimentary belt in Kerman province at the SE of Iran that is embedded in the Urumieh-Dokhtar Magmatic Assemblage arc (UDMA) is chosen to integrate broad evidential layers in the region of prospect. The studied area has high potential of ore mineral occurrences especially porphyry copper/molybdenum and the generated mineral potential maps aim to outline new prospect zones for further investigation in future. Two evidential layers of the downward continued aeromagnetic data and its analytic signal filter are prepared to be incorporated in fusion process as geophysical plausible footprints of the porphyry type mineralization. The low values of the apparent resistivity layer calculated from the airborne frequency domain electromagnetic data are also used as an electrical criterion in this investigation. Four remote sensing evidential layers of argillic, phyllic, propylitic and hydroxyl alterations were extracted from ASTER images in order to map the altered areas associated with porphyry type deposits, whilst the ETM+ satellite imagery data were used as well to map iron oxide layer. Since potassium alteration is generally the mainstay of porphyry ore mineralization, the airborne potassium radiometry data was used. The geochemical layers of Cu/B/Pb/Zn elements and the first component of PCA analysis were considered as powerful traces to prepare final maps. The conventional, adjusted and modified variants of the TOPSIS method produced three mineral potential maps, in which the outputs indicate adequately matching of high potential zones with previous working and active mines in the region.

Terahertz imaging systems: a non-invasive technique for the analysis of paintings

NASA Astrophysics Data System (ADS)

Fukunaga, K.; Hosako, I.; Duling, I. N., III; Picollo, M.

2009-07-01

Terahertz (THz) imaging is an emerging technique for non-invasive analysis. Since THz waves can penetrate opaque materials, various imaging systems that use THz waves have been developed to detect, for instance, concealed weapons, illegal drugs, and defects in polymer products. The absorption of THz waves by water is extremely strong, and hence, THz waves can be used to monitor the water content in various objects. THz imaging can be performed either by transmission or by reflection of THz waves. In particular, time domain reflection imaging uses THz pulses that propagate in specimens, and in this technique, pulses reflected from the surface and from the internal boundaries of the specimen are detected. In general, the internal structure is observed in crosssectional images obtained using micro-specimens taken from the work that is being analysed. On the other hand, in THz time-domain imaging, a map of the layer of interest can be easily obtained without collecting any samples. When realtime imaging is required, for example, in the investigation of the effect of a solvent or during the monitoring of water content, a THz camera can be used. The first application of THz time-domain imaging in the analysis of a historical tempera masterpiece was performed on the panel painting Polittico di Badia by Giotto, of the permanent collection of the Uffizi Gallery. The results of that analysis revealed that the work is composed of two layers of gypsum, with a canvas between these layers. In the paint layer, gold foils covered by paint were clearly observed, and the consumption or ageing of gold could be estimated by noting the amount of reflection. These results prove that THz imaging can yield useful information for conservation and restoration purposes.

Big data; sensor networks and remotely-sensed data for mapping; feature extraction from lidar

NASA Astrophysics Data System (ADS)

Tlhabano, Lorato

2018-05-01

Unmanned aerial vehicles (UAVs) can be used for mapping in the close range domain, combining aerial and terrestrial photogrammetry and now the emergence of affordable platforms to carry these technologies has opened up new opportunities for mapping and modeling cadastral boundaries. At the current state mainly low cost UAVs fitted with sensors are used in mapping projects with low budgets, the amount of data produced by the UAVs can be enormous hence the need for big data techniques' and concepts. The past couple of years have witnessed the dramatic rise of low-cost UAVs fitted with high tech Lidar sensors and as such the UAVS have now reached a level of practical reliability and professionalism which allow the use of these systems as mapping platforms. UAV based mapping provides not only the required accuracy with respect to cadastral laws and policies as well as requirements for feature extraction from the data sets and maps produced, UAVs are also competitive to other measurement technologies in terms of economic aspects. In the following an overview on how the various technologies of UAVs, big data concepts and lidar sensor technologies can work together to revolutionize cadastral mapping particularly in Africa and as a test case Botswana in particular will be used to investigate these technologies. These technologies can be combined to efficiently provide cadastral mapping in difficult to reach areas and over large areas of land similar to the Land Administration Procedures, Capacity and Systems (LAPCAS) exercise which was recently undertaken by the Botswana government, we will show how the uses of UAVS fitted with lidar sensor and utilizing big data concepts could have reduced not only costs and time for our government but also how UAVS could have provided more detailed cadastral maps.

2D Flood Modelling Using Advanced Terrain Analysis Techniques And A Fully Continuous DEM-Based Rainfall-Runoff Algorithm

NASA Astrophysics Data System (ADS)

Nardi, F.; Grimaldi, S.; Petroselli, A.

2012-12-01

Remotely sensed Digital Elevation Models (DEMs), largely available at high resolution, and advanced terrain analysis techniques built in Geographic Information Systems (GIS), provide unique opportunities for DEM-based hydrologic and hydraulic modelling in data-scarce river basins paving the way for flood mapping at the global scale. This research is based on the implementation of a fully continuous hydrologic-hydraulic modelling optimized for ungauged basins with limited river flow measurements. The proposed procedure is characterized by a rainfall generator that feeds a continuous rainfall-runoff model producing flow time series that are routed along the channel using a bidimensional hydraulic model for the detailed representation of the inundation process. The main advantage of the proposed approach is the characterization of the entire physical process during hydrologic extreme events of channel runoff generation, propagation, and overland flow within the floodplain domain. This physically-based model neglects the need for synthetic design hyetograph and hydrograph estimation that constitute the main source of subjective analysis and uncertainty of standard methods for flood mapping. Selected case studies show results and performances of the proposed procedure as respect to standard event-based approaches.

Going to the source: creating a citizenship outcome measure by community-based participatory research methods.

PubMed

Rowe, Michael; Clayton, Ashley; Benedict, Patricia; Bellamy, Chyrell; Antunes, Kimberly; Miller, Rebecca; Pelletier, Jean-Francois; Stern, Erica; O'Connell, Maria J

2012-01-01

This study used participatory methods and concept-mapping techniques to develop a greater understanding of the construct of citizenship and an instrument to assess the degree to which individuals, particularly those with psychiatric disorders, perceive themselves to be citizens in a multifaceted sense (that is, not in a simply legal sense). Participants were persons with recent experience of receiving public mental health services, having criminal justice charges, having a serious general medical illness, or having more than one of these "life disruptions," along with persons who had not experienced any of these disruptions. Community-based participatory methods, including a co-researcher team of persons with experiences of mental illness and other life disruptions, were employed. Procedures included conducting focus groups with each life disruption (or no disruption) group to generate statements about the meaning of citizenship (N = 75 participants); reducing the generated statements to 100 items and holding concept-mapping sessions with participants from the five stakeholder groups (N = 66 participants) to categorize and rate each item in terms of importance and access; analyzing concept-mapping data to produce citizenship domains; and developing a pilot instrument of citizenship. Multidimensional scaling and hierarchical cluster analysis revealed seven primary domains of citizenship: personal responsibilities, government and infrastructure, caring for self and others, civil rights, legal rights, choices, and world stewardship. Forty-six items were identified for inclusion in the citizenship measure. Citizenship is a multidimensional construct encompassing the degree to which individuals with different life experiences perceive inclusion or involvement across a variety of activities and concepts.

What Four Million Mappings Can Tell You about Two Hundred Ontologies

NASA Astrophysics Data System (ADS)

Ghazvinian, Amir; Noy, Natalya F.; Jonquet, Clement; Shah, Nigam; Musen, Mark A.

The field of biomedicine has embraced the Semantic Web probably more than any other field. As a result, there is a large number of biomedical ontologies covering overlapping areas of the field. We have developed BioPortal—an open community-based repository of biomedical ontologies. We analyzed ontologies and terminologies in BioPortal and the Unified Medical Language System (UMLS), creating more than 4 million mappings between concepts in these ontologies and terminologies based on the lexical similarity of concept names and synonyms. We then analyzed the mappings and what they tell us about the ontologies themselves, the structure of the ontology repository, and the ways in which the mappings can help in the process of ontology design and evaluation. For example, we can use the mappings to guide users who are new to a field to the most pertinent ontologies in that field, to identify areas of the domain that are not covered sufficiently by the ontologies in the repository, and to identify which ontologies will serve well as background knowledge in domain-specific tools. While we used a specific (but large) ontology repository for the study, we believe that the lessons we learned about the value of a large-scale set of mappings to ontology users and developers are general and apply in many other domains.

3D topology of orientation columns in visual cortex revealed by functional optical coherence tomography.

PubMed

Nakamichi, Yu; Kalatsky, Valery A; Watanabe, Hideyuki; Sato, Takayuki; Rajagopalan, Uma Maheswari; Tanifuji, Manabu

2018-04-01

Orientation tuning is a canonical neuronal response property of six-layer visual cortex that is encoded in pinwheel structures with center orientation singularities. Optical imaging of intrinsic signals enables us to map these surface two-dimensional (2D) structures, whereas lack of appropriate techniques has not allowed us to visualize depth structures of orientation coding. In the present study, we performed functional optical coherence tomography (fOCT), a technique capable of acquiring a 3D map of the intrinsic signals, to study the topology of orientation coding inside the cat visual cortex. With this technique, for the first time, we visualized columnar assemblies in orientation coding that had been predicted from electrophysiological recordings. In addition, we found that the columnar structures were largely distorted around pinwheel centers: center singularities were not rigid straight lines running perpendicularly to the cortical surface but formed twisted string-like structures inside the cortex that turned and extended horizontally through the cortex. Looping singularities were observed with their respective termini accessing the same cortical surface via clockwise and counterclockwise orientation pinwheels. These results suggest that a 3D topology of orientation coding cannot be fully anticipated from 2D surface measurements. Moreover, the findings demonstrate the utility of fOCT as an in vivo mesoscale imaging method for mapping functional response properties of cortex in the depth axis. NEW & NOTEWORTHY We used functional optical coherence tomography (fOCT) to visualize three-dimensional structure of the orientation columns with millimeter range and micrometer spatial resolution. We validated vertically elongated columnar structure in iso-orientation domains. The columnar structure was distorted around pinwheel centers. An orientation singularity formed a string with tortuous trajectories inside the cortex and connected clockwise and counterclockwise pinwheel centers in the surface orientation map. The results were confirmed by comparisons with conventional optical imaging and electrophysiological recordings.

Mountain cartography: revival of a classic domain

NASA Astrophysics Data System (ADS)

Häberling, Christian; Hurni, Lorenz

The abstract representation of landscape objects such as mountain peaks, valleys, river networks, lakes, cultivated land and nonproductive areas (forests, pastures, boulder fields, glaciers), settlement areas, infrastructure and traffic networks has been the main concept behind all kind of maps for a long time. For over 300 years, mountain regions became an appropriate subject to be extensively explored and mapped. Together with the growing importance of mountainous areas, the demand for adequate cartographic representations with respect to its contents, graphic design and the presentation media has given new life to a classic domain of cartography: Mountain cartography. This paper gives an overview of the development and the current state of mountain cartography. After a brief description of the beginnings and the historic achievements, basic concepts of cartography such as map purpose, data management, cartographic design and map production and their application in modern mountain cartography are summarised. The paper then provides an overview of different kinds of cartographic representations in mountain cartography like topographic maps, maps derived from Geographical Information Systems (GIS) data, image maps, animations, perspective views and personalised maps. Finally, selected examples of modern mountain map applications are presented.

The Effectiveness of an Online Knowledge Map Instructional Presentation

ERIC Educational Resources Information Center

Foor, Jamie L.

2011-01-01

In this study, I investigated the effectiveness of the knowledge map (k-map) instructional strategy compared to a text-based presentation in an online environment. K-maps consist of node-link representations of concepts that together form the content of a topic or domain. The benefits of using k-maps are that concepts and ideas are represented as…

A web-based system architecture for ontology-based data integration in the domain of IT benchmarking

NASA Astrophysics Data System (ADS)

Pfaff, Matthias; Krcmar, Helmut

2018-03-01

In the domain of IT benchmarking (ITBM), a variety of data and information are collected. Although these data serve as the basis for business analyses, no unified semantic representation of such data yet exists. Consequently, data analysis across different distributed data sets and different benchmarks is almost impossible. This paper presents a system architecture and prototypical implementation for an integrated data management of distributed databases based on a domain-specific ontology. To preserve the semantic meaning of the data, the ITBM ontology is linked to data sources and functions as the central concept for database access. Thus, additional databases can be integrated by linking them to this domain-specific ontology and are directly available for further business analyses. Moreover, the web-based system supports the process of mapping ontology concepts to external databases by introducing a semi-automatic mapping recommender and by visualizing possible mapping candidates. The system also provides a natural language interface to easily query linked databases. The expected result of this ontology-based approach of knowledge representation and data access is an increase in knowledge and data sharing in this domain, which will enhance existing business analysis methods.

Automated object-based classification of topography from SRTM data

PubMed Central

Drăguţ, Lucian; Eisank, Clemens

2012-01-01

We introduce an object-based method to automatically classify topography from SRTM data. The new method relies on the concept of decomposing land-surface complexity into more homogeneous domains. An elevation layer is automatically segmented and classified at three scale levels that represent domains of complexity by using self-adaptive, data-driven techniques. For each domain, scales in the data are detected with the help of local variance and segmentation is performed at these appropriate scales. Objects resulting from segmentation are partitioned into sub-domains based on thresholds given by the mean values of elevation and standard deviation of elevation respectively. Results resemble reasonably patterns of existing global and regional classifications, displaying a level of detail close to manually drawn maps. Statistical evaluation indicates that most of classes satisfy the regionalization requirements of maximizing internal homogeneity while minimizing external homogeneity. Most objects have boundaries matching natural discontinuities at regional level. The method is simple and fully automated. The input data consist of only one layer, which does not need any pre-processing. Both segmentation and classification rely on only two parameters: elevation and standard deviation of elevation. The methodology is implemented as a customized process for the eCognition® software, available as online download. The results are embedded in a web application with functionalities of visualization and download. PMID:22485060

Automated object-based classification of topography from SRTM data

NASA Astrophysics Data System (ADS)

Drăguţ, Lucian; Eisank, Clemens

2012-03-01

We introduce an object-based method to automatically classify topography from SRTM data. The new method relies on the concept of decomposing land-surface complexity into more homogeneous domains. An elevation layer is automatically segmented and classified at three scale levels that represent domains of complexity by using self-adaptive, data-driven techniques. For each domain, scales in the data are detected with the help of local variance and segmentation is performed at these appropriate scales. Objects resulting from segmentation are partitioned into sub-domains based on thresholds given by the mean values of elevation and standard deviation of elevation respectively. Results resemble reasonably patterns of existing global and regional classifications, displaying a level of detail close to manually drawn maps. Statistical evaluation indicates that most of classes satisfy the regionalization requirements of maximizing internal homogeneity while minimizing external homogeneity. Most objects have boundaries matching natural discontinuities at regional level. The method is simple and fully automated. The input data consist of only one layer, which does not need any pre-processing. Both segmentation and classification rely on only two parameters: elevation and standard deviation of elevation. The methodology is implemented as a customized process for the eCognition® software, available as online download. The results are embedded in a web application with functionalities of visualization and download.

Effect of screw threading dislocations and inverse domain boundaries in GaN on the shape of reciprocal-space maps.

PubMed

Barchuk, Mykhailo; Motylenko, Mykhaylo; Lukin, Gleb; Pätzold, Olf; Rafaja, David

2017-04-01

The microstructure of polar GaN layers, grown by upgraded high-temperature vapour phase epitaxy on [001]-oriented sapphire substrates, was studied by means of high-resolution X-ray diffraction and transmission electron microscopy. Systematic differences between reciprocal-space maps measured by X-ray diffraction and those which were simulated for different densities of threading dislocations revealed that threading dislocations are not the only microstructure defect in these GaN layers. Conventional dark-field transmission electron microscopy and convergent-beam electron diffraction detected vertical inversion domains as an additional microstructure feature. On a series of polar GaN layers with different proportions of threading dislocations and inversion domain boundaries, this contribution illustrates the capability and limitations of coplanar reciprocal-space mapping by X-ray diffraction to distinguish between these microstructure features.

Novel 3D ultrasound image-based biomarkers based on a feature selection from a 2D standardized vessel wall thickness map: a tool for sensitive assessment of therapies for carotid atherosclerosis

NASA Astrophysics Data System (ADS)

Chiu, Bernard; Li, Bing; Chow, Tommy W. S.

2013-09-01

With the advent of new therapies and management strategies for carotid atherosclerosis, there is a parallel need for measurement tools or biomarkers to evaluate the efficacy of these new strategies. 3D ultrasound has been shown to provide reproducible measurements of plaque area/volume and vessel wall volume. However, since carotid atherosclerosis is a focal disease that predominantly occurs at bifurcations, biomarkers based on local plaque change may be more sensitive than global volumetric measurements in demonstrating efficacy of new therapies. The ultimate goal of this paper is to develop a biomarker that is based on the local distribution of vessel-wall-plus-plaque thickness change (VWT-Change) that has occurred during the course of a clinical study. To allow comparison between different treatment groups, the VWT-Change distribution of each subject must first be mapped to a standardized domain. In this study, we developed a technique to map the 3D VWT-Change distribution to a 2D standardized template. We then applied a feature selection technique to identify regions on the 2D standardized map on which subjects in different treatment groups exhibit greater difference in VWT-Change. The proposed algorithm was applied to analyse the VWT-Change of 20 subjects in a placebo-controlled study of the effect of atorvastatin (Lipitor). The average VWT-Change for each subject was computed (i) over all points in the 2D map and (ii) over feature points only. For the average computed over all points, 97 subjects per group would be required to detect an effect size of 25% that of atorvastatin in a six-month study. The sample size is reduced to 25 subjects if the average were computed over feature points only. The introduction of this sensitive quantification technique for carotid atherosclerosis progression/regression would allow many proof-of-principle studies to be performed before a more costly and longer study involving a larger population is held to confirm the treatment efficacy.

Landscape features, standards, and semantics in U.S. national topographic mapping databases

USGS Publications Warehouse

Varanka, Dalia

2009-01-01

The objective of this paper is to examine the contrast between local, field-surveyed topographical representation and feature representation in digital, centralized databases and to clarify their ontological implications. The semantics of these two approaches are contrasted by examining the categorization of features by subject domains inherent to national topographic mapping. When comparing five USGS topographic mapping domain and feature lists, results indicate that multiple semantic meanings and ontology rules were applied to the initial digital database, but were lost as databases became more centralized at national scales, and common semantics were replaced by technological terms.

The efficacy of the 'mind map' study technique.

PubMed

Farrand, Paul; Hussain, Fearzana; Hennessy, Enid

2002-05-01

To examine the effectiveness of using the 'mind map' study technique to improve factual recall from written information. To obtain baseline data, subjects completed a short test based on a 600-word passage of text prior to being randomly allocated to form two groups: 'self-selected study technique' and 'mind map'. After a 30-minute interval the self-selected study technique group were exposed to the same passage of text previously seen and told to apply existing study techniques. Subjects in the mind map group were trained in the mind map technique and told to apply it to the passage of text. Recall was measured after an interfering task and a week later. Measures of motivation were taken. Barts and the London School of Medicine and Dentistry, University of London. 50 second- and third-year medical students. Recall of factual material improved for both the mind map and self-selected study technique groups at immediate test compared with baseline. However this improvement was only robust after a week for those in the mind map group. At 1 week, the factual knowledge in the mind map group was greater by 10% (adjusting for baseline) (95% CI -1% to 22%). However motivation for the technique used was lower in the mind map group; if motivation could have been made equal in the groups, the improvement with mind mapping would have been 15% (95% CI 3% to 27%). Mind maps provide an effective study technique when applied to written material. However before mind maps are generally adopted as a study technique, consideration has to be given towards ways of improving motivation amongst users.

Combined interpretation of multiple geophysical techniques: an archaeological case study

NASA Astrophysics Data System (ADS)

Riedl, S.; Reichmann, S.; Tronicke, J.; Lück, E.

2009-04-01

In order to locate and ascertain the dimensions of an ancient orangery, we explored an area of about 70 m x 60 m in the Rheinsberg Palace Garden (Germany) with multiple geophysical techniques. The Rheinsberg Park, situated about 100 km northwest of Berlin, Germany, was established by the Prussian emperors in the 18th century. Due to redesign of the architecture and the landscaping during the past 300 years, buildings were dismantled and detailed knowledge about some original buildings got lost. We surveyed an area close to a gazebo where, after historical sources, an orangery was planned around the year 1740. However, today it is not clear to what extent this plan has been realized and if remains of this building are still buried in the subsurface. Applied geophysical techniques include magnetic gradiometry, frequency domain electromagnetic (FDEM) and direct current (DC) resistivity mapping as well as ground penetrating radar (GPR). To get an overview of the site, we performed FDEM electrical conductivity mapping using an EM38 instrument and magnetic gradiometry with caesium magnetometers. Both data sets were collected with an in- and crossline data point spacing of ca. 10 cm and 50 cm, respectively. DC resistivity surveying was performed using a pole-pole electrode configuration with an electrode spacing of 1.5 m and a spacing of 1.0 m between individual readings. A 3-D GPR survey was conducted using 200 MHz antennae and in- and crossline spacing of ca. 10 cm and 40 cm, respectively. A standard processing sequence including 3-D migration was applied. A combined interpretation of all collected data sets illustrates that the magnetic gradient and the EM38 conductivity maps is are dominated by anomalies from metallic water pipes from belonging to the irrigation system of the park. The DC resistivity map outlines a rectangular area which might indicate the extension of a former building south of the gazebo. The 3-D GPR data set provides further insights about subsurface structures and relevant geometries. From this data set, we interpret the depth and the extent of foundation and wall remains in the southern and central part of the site indicating the extent of the old orangery. This case study clearly illustrates the benefit of using multiple geophysical methods in archaeological studies. It further illustrates the advantage of 3-D GPR surveying at sites where anthropogenic disturbances (such as metallic pipes and other utilities) might limit the applicability of commonly applied mapping techniques such as magnetic gradiometry or EM38 conductivity mapping.

Modeling software systems by domains

NASA Technical Reports Server (NTRS)

Dippolito, Richard; Lee, Kenneth

1992-01-01

The Software Architectures Engineering (SAE) Project at the Software Engineering Institute (SEI) has developed engineering modeling techniques that both reduce the complexity of software for domain-specific computer systems and result in systems that are easier to build and maintain. These techniques allow maximum freedom for system developers to apply their domain expertise to software. We have applied these techniques to several types of applications, including training simulators operating in real time, engineering simulators operating in non-real time, and real-time embedded computer systems. Our modeling techniques result in software that mirrors both the complexity of the application and the domain knowledge requirements. We submit that the proper measure of software complexity reflects neither the number of software component units nor the code count, but the locus of and amount of domain knowledge. As a result of using these techniques, domain knowledge is isolated by fields of engineering expertise and removed from the concern of the software engineer. In this paper, we will describe kinds of domain expertise, describe engineering by domains, and provide relevant examples of software developed for simulator applications using the techniques.

A New Objective Technique for Verifying Mesoscale Numerical Weather Prediction Models

NASA Technical Reports Server (NTRS)

Case, Jonathan L.; Manobianco, John; Lane, John E.; Immer, Christopher D.

2003-01-01

This report presents a new objective technique to verify predictions of the sea-breeze phenomenon over east-central Florida by the Regional Atmospheric Modeling System (RAMS) mesoscale numerical weather prediction (NWP) model. The Contour Error Map (CEM) technique identifies sea-breeze transition times in objectively-analyzed grids of observed and forecast wind, verifies the forecast sea-breeze transition times against the observed times, and computes the mean post-sea breeze wind direction and speed to compare the observed and forecast winds behind the sea-breeze front. The CEM technique is superior to traditional objective verification techniques and previously-used subjective verification methodologies because: It is automated, requiring little manual intervention, It accounts for both spatial and temporal scales and variations, It accurately identifies and verifies the sea-breeze transition times, and It provides verification contour maps and simple statistical parameters for easy interpretation. The CEM uses a parallel lowpass boxcar filter and a high-order bandpass filter to identify the sea-breeze transition times in the observed and model grid points. Once the transition times are identified, CEM fits a Gaussian histogram function to the actual histogram of transition time differences between the model and observations. The fitted parameters of the Gaussian function subsequently explain the timing bias and variance of the timing differences across the valid comparison domain. Once the transition times are all identified at each grid point, the CEM computes the mean wind direction and speed during the remainder of the day for all times and grid points after the sea-breeze transition time. The CEM technique performed quite well when compared to independent meteorological assessments of the sea-breeze transition times and results from a previously published subjective evaluation. The algorithm correctly identified a forecast or observed sea-breeze occurrence or absence 93% of the time during the two- month evaluation period from July and August 2000. Nearly all failures in CEM were the result of complex precipitation features (observed or forecast) that contaminated the wind field, resulting in a false identification of a sea-breeze transition. A qualitative comparison between the CEM timing errors and the subjectively determined observed and forecast transition times indicate that the algorithm performed very well overall. Most discrepancies between the CEM results and the subjective analysis were again caused by observed or forecast areas of precipitation that led to complex wind patterns. The CEM also failed on a day when the observed sea- breeze transition affected only a very small portion of the verification domain. Based on the results of CEM, the RAMS tended to predict the onset and movement of the sea-breeze transition too early and/or quickly. The domain-wide timing biases provided by CEM indicated an early bias on 30 out of 37 days when both an observed and forecast sea breeze occurred over the same portions of the analysis domain. These results are consistent with previous subjective verifications of the RAMS sea breeze predictions. A comparison of the mean post-sea breeze winds indicate that RAMS has a positive wind-speed bias for .all days, which is also consistent with the early bias in the sea-breeze transition time since the higher wind speeds resulted in a faster inland penetration of the sea breeze compared to reality.

Electromagnetic Measurements in an Active Oilfield Environment

NASA Astrophysics Data System (ADS)

Weiss, C. J.; Aur, K. A.; Schramm, K. A.; Aldridge, D. F.; O'rourke, W. T.

2016-12-01

An important issue in oilfield development is mapping fracture distributions (either natural or man-made) controlling subsurface fluid flow. Although microseismic monitoring has been successful in constraining fracture system geometry and dynamics, accurate interpretation of microseismic data can be confounded by factors such as complex or poorly-understood velocity distributions, reactivation of previously unknown faults and fractures, and the problem of relating flow patterns to the cloud of hypocenter locations. For the particular problem of hydrocarbon production, the question of which fractures remain sufficiently "open" to allow economical fluid extraction is critical. As a supplement to microseismic analysis, we are investigating a novel electromagnetic (EM) technique for detecting and mapping hydraulic fractures in a hydrocarbon or geothermal reservoir by introducing an electrically conductive contrast agent into the fracturing fluid. In the field experiment presented here, a proppant-filled fracture zone is illuminated by a large engineered antenna consisting of an insulated current-carrying cable, grounded to `Earth' near the wellhead, and grounded at the other end to the steel-cased borehole near the target. Time-lapse measurements of horizontal electric field are subsequently made on Earth's surface to map the change in subsurface conductivity due to proppant emplacement. As predicted by 3D numerical modelling, observed differences in electric field values are very small. While these numbers are above the noise floor of electric field sensors, pervasive anthropogenic EM noise and regional-scale magnetotelluric signals make extraction of the differences from the observed time series especially difficult. We present field-acquired data on ambient EM noise in an active oilfield environment and demonstrate techniques for extracting the difference signal due to proppant emplacement. These techniques include classical spectral methods along with estimation of time-domain Green's function by regularized, linear least squares methods.

Web Mapping Architectures Based on Open Specifications and Free and Open Source Software in the Water Domain

NASA Astrophysics Data System (ADS)

Arias Muñoz, C.; Brovelli, M. A.; Kilsedar, C. E.; Moreno-Sanchez, R.; Oxoli, D.

2017-09-01

The availability of water-related data and information across different geographical and jurisdictional scales is of critical importance for the conservation and management of water resources in the 21st century. Today information assets are often found fragmented across multiple agencies that use incompatible data formats and procedures for data collection, storage, maintenance, analysis, and distribution. The growing adoption of Web mapping systems in the water domain is reducing the gap between data availability and its practical use and accessibility. Nevertheless, more attention must be given to the design and development of these systems to achieve high levels of interoperability and usability while fulfilling different end user informational needs. This paper first presents a brief overview of technologies used in the water domain, and then presents three examples of Web mapping architectures based on free and open source software (FOSS) and the use of open specifications (OS) that address different users' needs for data sharing, visualization, manipulation, scenario simulations, and map production. The purpose of the paper is to illustrate how the latest developments in OS for geospatial and water-related data collection, storage, and sharing, combined with the use of mature FOSS projects facilitate the creation of sophisticated interoperable Web-based information systems in the water domain.

The use of concept maps during knowledge elicitation in ontology development processes – the nutrigenomics use case

PubMed Central

Castro, Alexander Garcia; Rocca-Serra, Philippe; Stevens, Robert; Taylor, Chris; Nashar, Karim; Ragan, Mark A; Sansone, Susanna-Assunta

2006-01-01

Background Incorporation of ontologies into annotations has enabled 'semantic integration' of complex data, making explicit the knowledge within a certain field. One of the major bottlenecks in developing bio-ontologies is the lack of a unified methodology. Different methodologies have been proposed for different scenarios, but there is no agreed-upon standard methodology for building ontologies. The involvement of geographically distributed domain experts, the need for domain experts to lead the design process, the application of the ontologies and the life cycles of bio-ontologies are amongst the features not considered by previously proposed methodologies. Results Here, we present a methodology for developing ontologies within the biological domain. We describe our scenario, competency questions, results and milestones for each methodological stage. We introduce the use of concept maps during knowledge acquisition phases as a feasible transition between domain expert and knowledge engineer. Conclusion The contributions of this paper are the thorough description of the steps we suggest when building an ontology, example use of concept maps, consideration of applicability to the development of lower-level ontologies and application to decentralised environments. We have found that within our scenario conceptual maps played an important role in the development process. PMID:16725019

Interaction of the S100A6 mutant (C3S) with the V domain of the receptor for advanced glycation end products (RAGE)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mohan, Sepuru K., E-mail: mohansepuri@gmail.com; Gupta, Arun A., E-mail: ninja14gupta@gmail.com; Yu, Chin, E-mail: cyu.nthu@gmail.com

2013-05-03

Highlights: •The halo human S100A6 (C3S) NMR chemical shifts were assigned. •The interactions between S100A6m and RAGE V domain was investigated by ITC. •The residues involved in the S100A6m–RAGE V domain binding were mapped by {sup 1}H–{sup 15}N HSQC titration. •S100A6–RAGE V domain tetrameric complex model was generated from NMR studies. •The S100A6–RAGE V domain interface regions were elucidated based on HADDOCK model. -- Abstract: S100A6 is involved in several vital biological functions, such as calcium sensing and cell proliferation. It is a homodimeric protein that belongs to the S100 protein family. The receptor for advanced glycation end products (RAGE)more » has been shown to play a role in the progression of various disease conditions, such as diabetes and immune/inflammatory disorders. Information regarding the association of RAGE with S100 proteins at a molecular level is useful to understand the diversity of the RAGE signaling pathways. In this report, biomolecular NMR techniques were utilized for the resonance assignment of the C3S mutation in human S100A6 and characterizing its interaction with the RAGE V domain. Further binding affinity between S100A6m and the RAGE V domain was determined by isothermal titration calorimetric studies. HADDOCK was used to generate a heterotetramer model of the S100A6m–RAGE V domain complex. This model provides an important insights into the S100–RAGE cellular signaling pathway.« less

Mapping structural landmarks, ligand binding sites and missense mutations to the collagen IV heterotrimers predicts major functional domains, novel interactions and variation in phenotypes in inherited diseases affecting basement membranes

PubMed Central

Des Parkin, J.; San Antonio, James D.; Pedchenko, Vadim; Hudson, Billy; Jensen, Shane T.; Savige, Judy

2016-01-01

Collagen IV is the major protein found in basement membranes. It comprises 3 heterotrimers (α1α1α2, α3α4α5, and α5α5α6) that form distinct networks, and are responsible for membrane strength and integrity. We constructed linear maps of the collagen IV heterotrimers (‘interactomes’) that indicated major structural landmarks, known and predicted ligand-binding sites, and missense mutations, in order to identify functional and disease-associated domains, potential interactions between ligands, and genotype-phenotype relationships. The maps documented more than 30 known ligand-binding sites as well as motifs for integrins, heparin, von Willebrand factor (VWF), decorin and bone morphogenetic protein (BMP). They predicted functional domains for angiogenesis and haemostasis, and disease domains for autoimmunity, tumor growth and inhibition, infection and glycation. Cooperative ligand interactions were indicated by binding site proximity, for example, between integrins, matrix metalloproteinases and heparin. The maps indicated that mutations affecting major ligand-binding sites, for example for Von Hippel Lindau (VHL) protein in the α1 chain or integrins in the α5 chain, resulted in distinctive phenotypes (Hereditary Angiopathy, Nephropathy, Aneurysms and muscle Cramps (HANAC) syndrome, and early onset Alport syndrome respectively). These maps further our understanding of basement membrane biology and disease, and suggest novel membrane interactions, functions, and therapeutic targets. PMID:21280145

Can the theoretical domains framework account for the implementation of clinical quality interventions?

PubMed

Lipworth, Wendy; Taylor, Natalie; Braithwaite, Jeffrey

2013-12-21

The health care quality improvement movement is a complex enterprise. Implementing clinical quality initiatives requires attitude and behaviour change on the part of clinicians, but this has proven to be difficult. In an attempt to solve this kind of behavioural challenge, the theoretical domains framework (TDF) has been developed. The TDF consists of 14 domains from psychological and organisational theory said to influence behaviour change. No systematic research has been conducted into the ways in which clinical quality initiatives map on to the domains of the framework. We therefore conducted a qualitative mapping experiment to determine to what extent, and in what ways, the TDF is relevant to the implementation of clinical quality interventions. We conducted a thematic synthesis of the qualitative literature exploring clinicians' perceptions of various clinical quality interventions. We analysed and synthesised 50 studies in total, in five domains of clinical quality interventions: clinical quality interventions in general, structural interventions, audit-type interventions, interventions aimed at making practice more evidence-based, and risk management interventions. Data were analysed thematically, followed by synthesis of these themes into categories and concepts, which were then mapped to the domains of the TDF. Our results suggest that the TDF is highly relevant to the implementation of clinical quality interventions. It can be used to map most, if not all, of the attitudinal and behavioural barriers and facilitators of uptake of clinical quality interventions. Each of these 14 domains appeared to be relevant to many different types of clinical quality interventions. One possible additional domain might relate to perceived trustworthiness of those instituting clinical quality interventions. The TDF can be usefully applied to a wide range of clinical quality interventions. Because all 14 of the domains emerged as relevant, and we did not identify any obvious differences between different kinds of clinical quality interventions, our findings support an initially broad approach to identifying barriers and facilitators, followed by a "drilling down" to what is most contextually salient. In future, it may be possible to establish a model of clinical quality policy implementation using the TDF.

Can the theoretical domains framework account for the implementation of clinical quality interventions?

PubMed Central

2013-01-01

Background The health care quality improvement movement is a complex enterprise. Implementing clinical quality initiatives requires attitude and behaviour change on the part of clinicians, but this has proven to be difficult. In an attempt to solve this kind of behavioural challenge, the theoretical domains framework (TDF) has been developed. The TDF consists of 14 domains from psychological and organisational theory said to influence behaviour change. No systematic research has been conducted into the ways in which clinical quality initiatives map on to the domains of the framework. We therefore conducted a qualitative mapping experiment to determine to what extent, and in what ways, the TDF is relevant to the implementation of clinical quality interventions. Methods We conducted a thematic synthesis of the qualitative literature exploring clinicians’ perceptions of various clinical quality interventions. We analysed and synthesised 50 studies in total, in five domains of clinical quality interventions: clinical quality interventions in general, structural interventions, audit-type interventions, interventions aimed at making practice more evidence-based, and risk management interventions. Data were analysed thematically, followed by synthesis of these themes into categories and concepts, which were then mapped to the domains of the TDF. Results Our results suggest that the TDF is highly relevant to the implementation of clinical quality interventions. It can be used to map most, if not all, of the attitudinal and behavioural barriers and facilitators of uptake of clinical quality interventions. Each of these 14 domains appeared to be relevant to many different types of clinical quality interventions. One possible additional domain might relate to perceived trustworthiness of those instituting clinical quality interventions. Conclusions The TDF can be usefully applied to a wide range of clinical quality interventions. Because all 14 of the domains emerged as relevant, and we did not identify any obvious differences between different kinds of clinical quality interventions, our findings support an initially broad approach to identifying barriers and facilitators, followed by a “drilling down” to what is most contextually salient. In future, it may be possible to establish a model of clinical quality policy implementation using the TDF. PMID:24359085

Wavelet analysis of polarization maps of polycrystalline biological fluids networks

NASA Astrophysics Data System (ADS)

Ushenko, Y. A.

2011-12-01

The optical model of human joints synovial fluid is proposed. The statistic (statistic moments), correlation (autocorrelation function) and self-similar (Log-Log dependencies of power spectrum) structure of polarization two-dimensional distributions (polarization maps) of synovial fluid has been analyzed. It has been shown that differentiation of polarization maps of joint synovial fluid with different physiological state samples is expected of scale-discriminative analysis. To mark out of small-scale domain structure of synovial fluid polarization maps, the wavelet analysis has been used. The set of parameters, which characterize statistic, correlation and self-similar structure of wavelet coefficients' distributions of different scales of polarization domains for diagnostics and differentiation of polycrystalline network transformation connected with the pathological processes, has been determined.

M-and-C Domain Map Maker: an environment complimenting MDE with M-and-C knowledge and ensuring solution completeness

NASA Astrophysics Data System (ADS)

Patwari, Puneet; Choudhury, Subhrojyoti R.; Banerjee, Amar; Swaminathan, N.; Pandey, Shreya

2016-07-01

Model Driven Engineering (MDE) as a key driver to reduce development cost of M&C systems is beginning to find acceptance across scientific instruments such as Radio Telescopes and Nuclear Reactors. Such projects are adopting it to reduce time to integrate, test and simulate their individual controllers and increase reusability and traceability in the process. The creation and maintenance of models is still a significant challenge to realizing MDE benefits. Creating domain-specific modelling environments reduces the barriers, and we have been working along these lines, creating a domain-specific language and environment based on an M&C knowledge model. However, large projects involve several such domains, and there is still a need to interconnect the domain models, in order to ensure modelling completeness. This paper presents a knowledge-centric approach to doing that, by creating a generic system model that underlies the individual domain knowledge models. We present our vision for M&C Domain Map Maker, a set of processes and tools that enables explication of domain knowledge in terms of domain models with mutual consistency relationships to aid MDE.

Elasticity reconstruction: Beyond the assumption of local homogeneity

NASA Astrophysics Data System (ADS)

Sinkus, Ralph; Daire, Jean-Luc; Van Beers, Bernard E.; Vilgrain, Valerie

2010-07-01

Elasticity imaging is a novel domain which is currently gaining significant interest in the medical field. Most inversion techniques are based on the homogeneity assumption, i.e. the local spatial derivatives of the complex-shear modulus are ignored. This analysis presents an analytic approach in order to overcome this limitation, i.e. first order spatial derivatives of the real-part of the complex-shear modulus are taken into account. Resulting distributions in a gauged breast lesion phantom agree very well with the theoretical expectations. An in-vivo example of a cholangiocarcinoma demonstrates that the new approach provides maps of the viscoelastic properties which agree much better with expectations from anatomy.

The structure of polarization maps of skin histological sections in the Fourier domain for the tasks of benign and malignant formations differentiation

NASA Astrophysics Data System (ADS)

Ushenko, V. A.; Dubolazov, A. V.; Savich, V. O.; Novakovskaya, O. Y.; Olar, O. V.; Marchuk, Y. F.

2015-02-01

The optical model of birefringent networks of biological tissues is presented. The technique of Fourier polarimetry for selection of manifestations of linear and circular birefringence of protein fibrils is suggested. The results of investigations of statistical (statistical moments of the 1st-4th orders), correlation (dispersion and excess of autocorrelation functions) and scalar-self-similar (logarithmic dependencies of power spectra) structure of Fourier spectra of polarization azimuths distribution of laser images of skin samples are presented. The criteria of differentiation of postoperative biopsy of benign (keratoma) and malignant (adenocarcinoma) skin tumors are determined.

LoyalTracker: Visualizing Loyalty Dynamics in Search Engines.

PubMed

Shi, Conglei; Wu, Yingcai; Liu, Shixia; Zhou, Hong; Qu, Huamin

2014-12-01

The huge amount of user log data collected by search engine providers creates new opportunities to understand user loyalty and defection behavior at an unprecedented scale. However, this also poses a great challenge to analyze the behavior and glean insights into the complex, large data. In this paper, we introduce LoyalTracker, a visual analytics system to track user loyalty and switching behavior towards multiple search engines from the vast amount of user log data. We propose a new interactive visualization technique (flow view) based on a flow metaphor, which conveys a proper visual summary of the dynamics of user loyalty of thousands of users over time. Two other visualization techniques, a density map and a word cloud, are integrated to enable analysts to gain further insights into the patterns identified by the flow view. Case studies and the interview with domain experts are conducted to demonstrate the usefulness of our technique in understanding user loyalty and switching behavior in search engines.

Shallow landslide prediction and analysis with risk assessment using a spatial model in the coastal region in the state of São Paulo, Brazil

NASA Astrophysics Data System (ADS)

Camarinha, P. I. M.; Canavesi, V.; Alvalá, R. C. S.

2013-10-01

In Brazil, most of the disasters involving landslide occur in coastal regions, with population density concentrated on steep slopes. Thus, different approaches have been used to evaluate the landslide risk, although the greatest difficulty is related to the scarcity of spatial data with good quality. In this context, four cities located on the southeast coast of Brazil - Santos, Cubatão, Caraguatatuba and Ubatuba - in a region with the rough reliefs of the Serra do Mar and with a history of natural disasters were evaluated. Spatial prediction by fuzzy gamma technique was used for the landslide susceptibility mapping, considering environmental variables from data and software in the public domain. To validate the susceptibility mapping results, it was overlapped with risk sectors provided by the Geological Survey of Brazil (CPRM). A positive correlation was observed between the classes most susceptible and the location of these sectors. The results were also analyzed from the categorization of risk levels provided by CPRM. To compare the approach with other studies using landslide-scar maps, correlated indexes were evaluated, which also showed satisfactory results, thus indicating that the methodology presented is appropriate for risk assessment in urban areas and can be replicated to municipalities that do not have risk areas mapped.

Spatial-temporal three-dimensional ultrasound plane-by-plane active cavitation mapping for high-intensity focused ultrasound in free field and pulsatile flow.

PubMed

Ding, Ting; Hu, Hong; Bai, Chen; Guo, Shifang; Yang, Miao; Wang, Supin; Wan, Mingxi

2016-07-01

Cavitation plays important roles in almost all high-intensity focused ultrasound (HIFU) applications. However, current two-dimensional (2D) cavitation mapping could only provide cavitation activity in one plane. This study proposed a three-dimensional (3D) ultrasound plane-by-plane active cavitation mapping (3D-UPACM) for HIFU in free field and pulsatile flow. The acquisition of channel-domain raw radio-frequency (RF) data in 3D space was performed by sequential plane-by-plane 2D ultrafast active cavitation mapping. Between two adjacent unit locations, there was a waiting time to make cavitation nuclei distribution of the liquid back to the original state. The 3D cavitation map equivalent to the one detected at one time and over the entire volume could be reconstructed by Marching Cube algorithm. Minimum variance (MV) adaptive beamforming was combined with coherence factor (CF) weighting (MVCF) or compressive sensing (CS) method (MVCS) to process the raw RF data for improved beamforming or more rapid data processing. The feasibility of 3D-UPACM was demonstrated in tap-water and a phantom vessel with pulsatile flow. The time interval between temporal evolutions of cavitation bubble cloud could be several microseconds. MVCF beamformer had a signal-to-noise ratio (SNR) at 14.17dB higher, lateral and axial resolution at 2.88times and 1.88times, respectively, which were compared with those of B-mode active cavitation mapping. MVCS beamformer had only 14.94% time penalty of that of MVCF beamformer. This 3D-UPACM technique employs the linear array of a current ultrasound diagnosis system rather than a 2D array transducer to decrease the cost of the instrument. Moreover, although the application is limited by the requirement for a gassy fluid medium or a constant supply of new cavitation nuclei that allows replenishment of nuclei between HIFU exposures, this technique may exhibit a useful tool in 3D cavitation mapping for HIFU with high speed, precision and resolution, especially in a laboratory environment where more careful analysis may be required under controlled conditions. Copyright © 2016 Elsevier B.V. All rights reserved.

Incorporating maps of leaf chlorophyll in a thermal-based two-source energy balance scheme for mapping coupled fluxes of carbon and water exchange at a range of scales

NASA Astrophysics Data System (ADS)

Houborg, R.; Anderson, M. C.; Kustas, W. P.

2008-12-01

A light-use efficiency (LUE) based model of canopy resistance was recently implemented within a thermal- based Two-Source Energy Balance (TSEB) scheme facilitating coupled simulations of land-surface fluxes of water, energy and CO2 exchange from field to regional scales (Anderson et al., 2008). The LUE model component computes canopy-scale carbon assimilation and transpiration fluxes and incorporates LUE modifications from biome specific nominal values (Bn) in response to variations in humidity, CO2 concentration, temperature (soil and air), wind speed, and direct beam vs. diffuse light composition. Here we incorporate leaf chlorophyll content (Cab) as a determinant of spatial and temporal variations in Bn as Cab is related to key LUE modulating factors such as crop phenology, vegetation stress and photosynthetic capacity. A linear relationship between Bn and Cab, established from stand-level measurement of LUE for unstressed environmental conditions and a representative set of Cab values for a range of agricultural and natural vegetation groups, is used to distribute Bn over the modeling domain. The technique is tested for an agricultural area near Bushland, Texas by fusing reflective and thermal based remote sensing inputs from SPOT, Landsat, ASTER and aircraft sensor systems. Maps of LAI and Cab are generated by using at-sensor radiances in green, red and near-infrared wavelengths as input to a REGularized canopy reFLECtance (REGFLEC) modeling tool that couples leaf optics (PROSPECT), canopy reflectance (ACRM), and atmospheric radiative transfer (6SV1) model components. Modeled carbon and water fluxes are compared with eddy covariance measurements made in stands of cotton and with fluxes measured by an aircraft flying transects over irrigated and non-irrigated agricultural land and natural vegetation. The technique is flexible and scalable and is portable to continental scales using GOES and MODIS data products. The results demonstrate utility in combining remotely sensed observations in the reflective solar and thermal domains for estimating carbon and water fluxes within a coupled framework.

Ultra-Structure database design methodology for managing systems biology data and analyses

PubMed Central

Maier, Christopher W; Long, Jeffrey G; Hemminger, Bradley M; Giddings, Morgan C

2009-01-01

Background Modern, high-throughput biological experiments generate copious, heterogeneous, interconnected data sets. Research is dynamic, with frequently changing protocols, techniques, instruments, and file formats. Because of these factors, systems designed to manage and integrate modern biological data sets often end up as large, unwieldy databases that become difficult to maintain or evolve. The novel rule-based approach of the Ultra-Structure design methodology presents a potential solution to this problem. By representing both data and processes as formal rules within a database, an Ultra-Structure system constitutes a flexible framework that enables users to explicitly store domain knowledge in both a machine- and human-readable form. End users themselves can change the system's capabilities without programmer intervention, simply by altering database contents; no computer code or schemas need be modified. This provides flexibility in adapting to change, and allows integration of disparate, heterogenous data sets within a small core set of database tables, facilitating joint analysis and visualization without becoming unwieldy. Here, we examine the application of Ultra-Structure to our ongoing research program for the integration of large proteomic and genomic data sets (proteogenomic mapping). Results We transitioned our proteogenomic mapping information system from a traditional entity-relationship design to one based on Ultra-Structure. Our system integrates tandem mass spectrum data, genomic annotation sets, and spectrum/peptide mappings, all within a small, general framework implemented within a standard relational database system. General software procedures driven by user-modifiable rules can perform tasks such as logical deduction and location-based computations. The system is not tied specifically to proteogenomic research, but is rather designed to accommodate virtually any kind of biological research. Conclusion We find Ultra-Structure offers substantial benefits for biological information systems, the largest being the integration of diverse information sources into a common framework. This facilitates systems biology research by integrating data from disparate high-throughput techniques. It also enables us to readily incorporate new data types, sources, and domain knowledge with no change to the database structure or associated computer code. Ultra-Structure may be a significant step towards solving the hard problem of data management and integration in the systems biology era. PMID:19691849

A method for age-matched OCT angiography deviation mapping in the assessment of disease- related changes to the radial peripapillary capillaries.

PubMed

Pinhas, Alexander; Linderman, Rachel; Mo, Shelley; Krawitz, Brian D; Geyman, Lawrence S; Carroll, Joseph; Rosen, Richard B; Chui, Toco Y

2018-01-01

To present a method for age-matched deviation mapping in the assessment of disease-related changes to the radial peripapillary capillaries (RPCs). We reviewed 4.5x4.5mm en face peripapillary OCT-A scans of 133 healthy control eyes (133 subjects, mean 41.5 yrs, range 11-82 yrs) and 4 eyes with distinct retinal pathologies, obtained using spectral-domain optical coherence tomography angiography. Statistical analysis was performed to evaluate the impact of age on RPC perfusion densities. RPC density group mean and standard deviation maps were generated for each decade of life. Deviation maps were created for the diseased eyes based on these maps. Large peripapillary vessel (LPV; noncapillary vessel) perfusion density was also studied for impact of age. Average healthy RPC density was 42.5±1.47%. ANOVA and pairwise Tukey-Kramer tests showed that RPC density in the ≥60yr group was significantly lower compared to RPC density in all younger decades of life (p<0.01). Average healthy LPV density was 21.5±3.07%. Linear regression models indicated that LPV density decreased with age, however ANOVA and pairwise Tukey-Kramer tests did not reach statistical significance. Deviation mapping enabled us to quantitatively and visually elucidate the significance of RPC density changes in disease. It is important to consider changes that occur with aging when analyzing RPC and LPV density changes in disease. RPC density, coupled with age-matched deviation mapping techniques, represents a potentially clinically useful method in detecting changes to peripapillary perfusion in disease.

Photo-irradiation paradigm: Mapping a remarkable facile technique used for advanced drug, gene and cell delivery.

PubMed

Shaker, Mohamed A; Younes, Husam M

2015-11-10

Undoubtedly, the progression of photo-irradiation technique has provided a smart engineering tool for the state-of-the-art biomaterials that guide the biomedical and therapeutic domains for promoting the modern pharmaceutical industry. Many investigators had exploited such a potential technique to create/ameliorate numerous pharmaceutical carriers. These carriers show promising applications that vary from small drug to therapeutic protein delivery and from gene to living cell encapsulation design. Harmony between the properties of precisely engineered precursors and the formed network structure broadens the investigator's intellect for both brilliant creations and effective applications. As well, controlling photo-curing at the formulation level, through manipulating the absorption of light stimuli, photoinitiator system and photo-responsive precursor, facilitates the exploration of novel distinctive biomaterials. Discussion of utilizing different photo-curing procedures in designing/formulation of different pharmaceutical carriers is the main emphasis of this review. In addition, recent applications of these intelligent techniques in targeted, controlled, and sustained drug delivery with understanding of photo-irradiation concept and mechanism are illustrated. Copyright © 2015 Elsevier B.V. All rights reserved.

Applicability of active infrared thermography for screening of human breast: a numerical study.

PubMed

Dua, Geetika; Mulaveesala, Ravibabu

2018-03-01

Active infrared thermography is a fast, painless, noncontact, and noninvasive imaging method, complementary to mammography, ultrasound, and magnetic resonance imaging methods for early diagnosis of breast cancer. This technique plays an important role in early detection of breast cancer to women of all ages, including pregnant or nursing women, with different sizes of breast, irrespective of either fatty or dense breast. This proposed complementary technique makes use of infrared emission emanating from the breast. Emanating radiations from the surface of the breast under test are detected with an infrared camera to map the thermal gradients over it, in order to reveal hidden tumors inside it. One of the reliable active infrared thermographic technique, linear frequency modulated thermal wave imaging is adopted to detect tumors present inside the breast. Further, phase and amplitude images are constructed using frequency and time-domain data analysis schemes. Obtained results show the potential of the proposed technique for early diagnosis of breast cancer in fatty as well as dense breasts. (2018) COPYRIGHT Society of Photo-Optical Instrumentation Engineers (SPIE).

Crustal structure of the northern Menderes Massif, western Turkey, imaged by joint gravity and magnetic inversion

NASA Astrophysics Data System (ADS)

Gessner, Klaus; Gallardo, Luis A.; Wedin, Francis; Sener, Kerim

2016-10-01

In western Anatolia, the Anatolide domain of the Tethyan orogen is exposed in one of the Earth's largest metamorphic core complexes, the Menderes Massif. The Menderes Massif experienced a two-stage exhumation: tectonic denudation in the footwall of a north-directed Miocene extensional detachment, followed by fragmentation by E-W and NW-SE-trending graben systems. Along the northern boundary of the core complex, the tectonic units of the Vardar-Izmir-Ankara suture zone overly the stage one footwall of the core complex, the northern Menderes Massif. In this study, we explore the structure of the upper crust in the northern Menderes Massif with cross-gradient joint inversion of gravity and aeromagnetic data along a series of 10-km-deep profiles. Our inversions, which are based on gravity and aeromagnetic measurements and require no geological and petrophysical constraints, reveal the salient features of the Earth's upper crust. We image the northern Menderes Massif as a relatively homogenous domain of low magnetization and medium to high density, with local anomalies related to the effect of interspersed igneous bodies and shallow basins. In contrast, both the northern and western boundaries of the northern Menderes Massif stand out as domains where dense mafic, metasedimentary and ultramafic domains with a weak magnetic signature alternate with low-density igneous complexes with high magnetization. With our technique, we are able to delineate Miocene basins and igneous complexes, and map the boundary between intermediate to mafic-dominated subduction-accretion units of the suture zone and the underlying felsic crust of the Menderes Massif. We demonstrate that joint gravity and magnetic inversion are not only capable of imaging local and regional changes in crustal composition, but can also be used to map discontinuities of geodynamic significance such as the Vardar-Izmir-Ankara suture and the West Anatolia Transfer Zone.

A saliency-based approach to detection of infrared target

NASA Astrophysics Data System (ADS)

Chen, Yanfei; Sang, Nong; Dan, Zhiping

2013-10-01

Automatic target detection in infrared images is a hot research field of national defense technology. We propose a new saliency-based infrared target detection model in this paper, which is based on the fact that human focus of attention is directed towards the relevant target to interpret the most promising information. For a given image, the convolution of the image log amplitude spectrum with a low-pass Gaussian kernel of an appropriate scale is equivalent to an image saliency detector in the frequency domain. At the same time, orientation and shape features extracted are combined into a saliency map in the spatial domain. Our proposed model decides salient targets based on a final saliency map, which is generated by integration of the saliency maps in the frequency and spatial domain. At last, the size of each salient target is obtained by maximizing entropy of the final saliency map. Experimental results show that the proposed model can highlight both small and large salient regions in infrared image, as well as inhibit repeated distractors in cluttered image. In addition, its detecting efficiency has improved significantly.

Unsupervised Domain Adaptation with Multiple Acoustic Models

DTIC Science & Technology

2010-12-01

Discriminative MAP Adaptation Standard ML-MAP has been extended to incorporate discrim- inative training criteria such as MMI and MPE [10]. Dis- criminative MAP...smoothing variable I . For example, the MMI - MAP mean is given by ( mmi -map) jm = fnumjm (O) den jm(O)g+Djm̂jm + I (ml-map) jm f numjm den... MMI training, and Djm is the Gaussian-dependent parameter for the extended Baum-Welch (EBW) algorithm. MMI -MAP has been successfully applied in

Evaluating SPLASH-2 Applications Using MapReduce

NASA Astrophysics Data System (ADS)

Zhu, Shengkai; Xiao, Zhiwei; Chen, Haibo; Chen, Rong; Zhang, Weihua; Zang, Binyu

MapReduce has been prevalent for running data-parallel applications. By hiding other non-functionality parts such as parallelism, fault tolerance and load balance from programmers, MapReduce significantly simplifies the programming of large clusters. Due to the mentioned features of MapReduce above, researchers have also explored the use of MapReduce on other application domains, such as machine learning, textual retrieval and statistical translation, among others.

A study of mapping exogenous knowledge representations into CONFIG

NASA Technical Reports Server (NTRS)

Mayfield, Blayne E.

1992-01-01

Qualitative reasoning is reasoning with a small set of qualitative values that is an abstraction of a larger and perhaps infinite set of quantitative values. The use of qualitative and quantitative reasoning together holds great promise for performance improvement in applications that suffer from large and/or imprecise knowledge domains. Included among these applications are the modeling, simulation, analysis, and fault diagnosis of physical systems. Several research groups continue to discover and experiment with new qualitative representations and reasoning techniques. However, due to the diversity of these techniques, it is difficult for the programs produced to exchange system models easily. The availability of mappings to transform knowledge from the form used by one of these programs to that used by another would open the doors for comparative analysis of these programs in areas such as completeness, correctness, and performance. A group at the Johnson Space Center (JSC) is working to develop CONFIG, a prototype qualitative modeling, simulation, and analysis tool for fault diagnosis applications in the U.S. space program. The availability of knowledge mappings from the programs produced by other research groups to CONFIG may provide savings in CONFIG's development costs and time, and may improve CONFIG's performance. The study of such mappings is the purpose of the research described in this paper. Two other research groups that have worked with the JSC group in the past are the Northwest University Group and the University of Texas at Austin Group. The former has produced a qualitative reasoning tool named SIMGEN, and the latter has produced one named QSIM. Another program produced by the Austin group is CC, a preprocessor that permits users to develop input for eventual use by QSIM, but in a more natural format. CONFIG and CC are both based on a component-connection ontology, so a mapping from CC's knowledge representation to CONFIG's knowledge representation was chosen as the focus of this study. A mapping from CC to CONFIG was developed. Due to differences between the two programs, however, the mapping transforms some of the CC knowledge to CONFIG as documentation rather than as knowledge in a form useful to computation. The study suggests that it may be worthwhile to pursue the mappings further. By implementing the mapping as a program, actual comparisons of computational efficiency and quality of results can be made between the QSIM and CONFIG programs. A secondary study may reveal that the results of the two programs augment one another, contradict one another, or differ only slightly. If the latter, the qualitative reasoning techniques may be compared in other areas, such as computational efficiency.

Mapping flexible protein domains at subnanometer resolution with the atomic force microscope.

PubMed

Müller, D J; Fotiadis, D; Engel, A

1998-06-23

The mapping of flexible protein domains with the atomic force microscope is reviewed. Examples discussed are the bacteriorhodopsin from Halobacterium salinarum, the head-tail-connector from phage phi29, and the hexagonally packed intermediate layer from Deinococcus radiodurans which all were recorded in physiological buffer solution. All three proteins undergo reversible structural changes that are reflected in standard deviation maps calculated from aligned topographs of individual protein complexes. Depending on the lateral resolution (up to 0.8 nm) flexible surface regions can ultimately be correlated with individual polypeptide loops. In addition, multivariate statistical classification revealed the major conformations of the protein surface.

Structure-function analysis of the extracellular domain of the pneumococcal cell division site positioning protein MapZ

NASA Astrophysics Data System (ADS)

Manuse, Sylvie; Jean, Nicolas L.; Guinot, Mégane; Lavergne, Jean-Pierre; Laguri, Cédric; Bougault, Catherine M.; Vannieuwenhze, Michael S.; Grangeasse, Christophe; Simorre, Jean-Pierre

2016-06-01

Accurate placement of the bacterial division site is a prerequisite for the generation of two viable and identical daughter cells. In Streptococcus pneumoniae, the positive regulatory mechanism involving the membrane protein MapZ positions precisely the conserved cell division protein FtsZ at the cell centre. Here we characterize the structure of the extracellular domain of MapZ and show that it displays a bi-modular structure composed of two subdomains separated by a flexible serine-rich linker. We further demonstrate in vivo that the N-terminal subdomain serves as a pedestal for the C-terminal subdomain, which determines the ability of MapZ to mark the division site. The C-terminal subdomain displays a patch of conserved amino acids and we show that this patch defines a structural motif crucial for MapZ function. Altogether, this structure-function analysis of MapZ provides the first molecular characterization of a positive regulatory process of bacterial cell division.

Analyzing the Use of Concept Maps in Computer Science: A Systematic Mapping Study

ERIC Educational Resources Information Center

dos Santos, Vinicius; de Souza, Érica F.; Felizardo, Katia R; Vijaykumar, Nandamudi L.

2017-01-01

Context: concept Maps (CMs) enable the creation of a schematic representation of a domain knowledge. For this reason, CMs have been applied in different research areas, including Computer Science. Objective: the objective of this paper is to present the results of a systematic mapping study conducted to collect and evaluate existing research on…

Photo-multiplier Tube Based Hybrid MRI and Frequency Domain Fluorescence Tomography System for Small Animal Imaging

PubMed Central

Lin, Y; Ghijsen, M T; Gao, H; Liu, N; Nalcioglu, O; Gulsen, G

2014-01-01

Fluorescence tomography (FT) is a promising molecular imaging technique that can spatially resolve both fluorophore concentration and lifetime parameters. However, recovered fluorophore parameters highly depend on the size and depth of the object due to the ill-posedness of the FT inverse problem. Structural a priori information from another high spatial resolution imaging modality has been demonstrated to significantly improve FT reconstruction accuracy. In this study, we have constructed a combined magnetic resonance imaging (MRI) and FT system for small animal imaging. A photo-multiplier tube (PMT) is used as the detector to acquire frequency domain FT measurements. This is the first MR-compatible time-resolved FT system that can reconstruct both fluorescence concentration and lifetime maps simultaneously. The performance of the hybrid system is evaluated with phantom studies. Two different fluorophores, Indocyanine Green (ICG) and 3-3′ Diethylthiatricarbocyanine Iodide (DTTCI), which have similar excitation and emission spectra but different lifetimes, are utilized. The fluorescence concentration and lifetime maps are both reconstructed with and without the structural a priori information obtained from MRI for comparison. We show that the hybrid system can accurately recover both fluorescence intensity and lifetime within 10% error for two 4.2 mm-diameter cylindrical objects embedded in a 38 mm-diameter cylindrical phantom when MRI structural a priori information is utilized. PMID:21753235

Jamming Behavior of Domain Walls in an Antiferromagnetic Film

NASA Astrophysics Data System (ADS)

Sinha, Sunil

2014-03-01

Over the last few years, attempts have been made to unify many aspects of the freezing behavior of glasses, granular materials, gels, supercooled liquids, etc. into a general conceptual framework of what is called jamming behavior. This occurs when particles reach packing densities high enough that their motions become highly restricted. A general phase diagram has been proposed onto which various materials systems, e.g glasses or granular materials, can be mapped. We will discuss some recent applications of resonant and non-resonant soft X-ray Grazing Incidence Scattering to mesoscopic science, for example the study of magnetic domain wall fluctuations in thin films. For these studies, we use resonant magnetic x-ray scattering with a coherent photon beam and the technique of X-ray Photon Correlation Spectroscopy. find that at the ordering temperature the domains of an antiferromagnetic system, namely Dysprosium metal, behave very much also like a jammed system and their associated fluctuations exhibit behavior which exhibit some of the universal characteristics of jammed systems, such as non-exponential relaxation and Vogel-Fulcher type freezing. Work supported by Basic Energy Sciences, U.S. Dept. of Energy under Grant Number: DE-SC0003678.

Fourier-domain study of drift turbulence driven sheared flow in a laboratory plasma

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xu, M.; Tynan, G. R.; Holland, C.

2010-03-15

Frequency-resolved nonlinear internal and kinetic energy transfer rates have been measured in the Controlled Shear Decorrelation Experiment (CSDX) linear plasma device using a recently developed technique [Xu et al., Phys. Plasmas 16, 042312 (2009)]. The results clearly show a net kinetic energy transfer into the zonal flow frequency region, consistent with previous time-domain observations of turbulence-driven shear flows [Tynan et al., Plasma Phys. Controlled Fusion 48, S51 (2006)]. The experimentally measured dispersion relation has been used to map the frequency-resolved energy transfer rates into the wave number domain, which shows that the shear flow drive comes from midrange (k{sub t}hetarho{submore » S}>0.3) drift fluctuations, and the strongest flow drive comes from k{sub t}hetarho{sub S}approx =1 fluctuations. Linear growth rates have been inferred from a linearized Hasegawa-Wakatani model [Hasegawa et al., Phys. Fluids 22, 2122 (1979)], which indicates that the m=0 mode is linearly stable and the m=1-10 modes (corresponding to k{sub t}hetarho{sub S}>0.3) are linearly unstable for the n=1 and n=2 radial eigenmodes. This is consistent with our energy transfer measurements.« less

Integrating multi-omic features exploiting Chromosome Conformation Capture data.

PubMed

Merelli, Ivan; Tordini, Fabio; Drocco, Maurizio; Aldinucci, Marco; Liò, Pietro; Milanesi, Luciano

2015-01-01

The representation, integration, and interpretation of omic data is a complex task, in particular considering the huge amount of information that is daily produced in molecular biology laboratories all around the world. The reason is that sequencing data regarding expression profiles, methylation patterns, and chromatin domains is difficult to harmonize in a systems biology view, since genome browsers only allow coordinate-based representations, discarding functional clusters created by the spatial conformation of the DNA in the nucleus. In this context, recent progresses in high throughput molecular biology techniques and bioinformatics have provided insights into chromatin interactions on a larger scale and offer a formidable support for the interpretation of multi-omic data. In particular, a novel sequencing technique called Chromosome Conformation Capture allows the analysis of the chromosome organization in the cell's natural state. While performed genome wide, this technique is usually called Hi-C. Inspired by service applications such as Google Maps, we developed NuChart, an R package that integrates Hi-C data to describe the chromosomal neighborhood starting from the information about gene positions, with the possibility of mapping on the achieved graphs genomic features such as methylation patterns and histone modifications, along with expression profiles. In this paper we show the importance of the NuChart application for the integration of multi-omic data in a systems biology fashion, with particular interest in cytogenetic applications of these techniques. Moreover, we demonstrate how the integration of multi-omic data can provide useful information in understanding why genes are in certain specific positions inside the nucleus and how epigenetic patterns correlate with their expression.

MetaMapR: pathway independent metabolomic network analysis incorporating unknowns.

PubMed

Grapov, Dmitry; Wanichthanarak, Kwanjeera; Fiehn, Oliver

2015-08-15

Metabolic network mapping is a widely used approach for integration of metabolomic experimental results with biological domain knowledge. However, current approaches can be limited by biochemical domain or pathway knowledge which results in sparse disconnected graphs for real world metabolomic experiments. MetaMapR integrates enzymatic transformations with metabolite structural similarity, mass spectral similarity and empirical associations to generate richly connected metabolic networks. This open source, web-based or desktop software, written in the R programming language, leverages KEGG and PubChem databases to derive associations between metabolites even in cases where biochemical domain or molecular annotations are unknown. Network calculation is enhanced through an interface to the Chemical Translation System, which allows metabolite identifier translation between >200 common biochemical databases. Analysis results are presented as interactive visualizations or can be exported as high-quality graphics and numerical tables which can be imported into common network analysis and visualization tools. Freely available at http://dgrapov.github.io/MetaMapR/. Requires R and a modern web browser. Installation instructions, tutorials and application examples are available at http://dgrapov.github.io/MetaMapR/. ofiehn@ucdavis.edu. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Examining Cybersecurity of Cyberphysical Systems for Critical Infrastructures Through Work Domain Analysis.

PubMed

Wang, Hao; Lau, Nathan; Gerdes, Ryan M

2018-04-01

The aim of this study was to apply work domain analysis for cybersecurity assessment and design of supervisory control and data acquisition (SCADA) systems. Adoption of information and communication technology in cyberphysical systems (CPSs) for critical infrastructures enables automated and distributed control but introduces cybersecurity risk. Many CPSs employ SCADA industrial control systems that have become the target of cyberattacks, which inflict physical damage without use of force. Given that absolute security is not feasible for complex systems, cyberintrusions that introduce unanticipated events will occur; a proper response will in turn require human adaptive ability. Therefore, analysis techniques that can support security assessment and human factors engineering are invaluable for defending CPSs. We conducted work domain analysis using the abstraction hierarchy (AH) to model a generic SCADA implementation to identify the functional structures and means-ends relations. We then adopted a case study approach examining the Stuxnet cyberattack by developing and integrating AHs for the uranium enrichment process, SCADA implementation, and malware to investigate the interactions between the three aspects of cybersecurity in CPSs. The AHs for modeling a generic SCADA implementation and studying the Stuxnet cyberattack are useful for mapping attack vectors, identifying deficiencies in security processes and features, and evaluating proposed security solutions with respect to system objectives. Work domain analysis is an effective analytical method for studying cybersecurity of CPSs for critical infrastructures in a psychologically relevant manner. Work domain analysis should be applied to assess cybersecurity risk and inform engineering and user interface design.

Integrated In Silico-In Vitro Identification and Characterization of the SH3-Mediated Interaction between Human PTTG and its Cognate Partners in Medulloblastoma.

PubMed

Liu, Jiangang; Wang, Dapeng; Li, Yanyan; Yao, Hui; Zhang, Nan; Zhang, Xuewen; Zhong, Fangping; Huang, Yulun

2018-06-01

The human pituitary tumor-transforming gene is an oncogenic protein which serves as a central hub in the cellular signaling network of medulloblastoma. The protein contains two vicinal PxxP motifs at its C terminus that are potential binding sites of peptide-recognition SH3 domains. Here, a synthetic protocol that integrated in silico analysis and in vitro assay was described to identify the SH3-binding partners of pituitary tumor-transforming gene in the gene expression profile of medulloblastoma. In the procedure, a variety of structurally diverse, non-redundant SH3 domains with high gene expression in medulloblastoma were compiled, and their three-dimensional structures were either manually retrieved from the protein data bank database or computationally modeled through bioinformatics technique. The binding capability of these domains towards the two PxxP-containing peptides m1p: 161 LGPPSPVK 168 and m2p: 168 KMPSPPWE 175 of pituitary tumor-transforming gene were ranked by structure-based scoring and fluorescence-based assay. Consequently, a number of SH3 domains, including MAP3K and PI3K, were found to have moderate or high affinity for m1p and/or m2p. Interestingly, the two overlapping peptides exhibits a distinct binding profile to these identified domain partners, suggesting that the binding selectivity of m1p and m2p is optimized across the medulloblastoma expression spectrum by competing for domain candidates. In addition, two redesigned versions of m1p peptide ware obtained via a structure-based rational mutation approach, which exhibited an increased affinity for the domain as compared to native peptide.

Identification of RFLP and NBS/PK profiling markers for disease resistance loci in genetic maps of oats.

PubMed

Sanz, M J; Loarce, Y; Fominaya, A; Vossen, J H; Ferrer, E

2013-01-01

Two of the domains most widely shared among R genes are the nucleotide binding site (NBS) and protein kinase (PK) domains. The present study describes and maps a number of new oat resistance gene analogues (RGAs) with two purposes in mind: (1) to identify genetic regions that contain R genes and (2) to determine whether RGAs can be used as molecular markers for qualitative loci and for QTLs affording resistance to Puccinia coronata. Such genes have been mapped in the diploid A. strigosa × A. wiestii (Asw map) and the hexaploid MN841801-1 × Noble-2 (MN map). Genomic and cDNA NBS-RGA probes from oat, barley and wheat were used to produce RFLPs and to obtain markers by motif-directed profiling based on the NBS (NBS profiling) and PK (PK profiling) domains. The efficiency of primers used in NBS/PK profiling to amplify RGA fragments was assessed by sequencing individual marker bands derived from genomic and cDNA fragments. The positions of 184 markers were identified in the Asw map, while those for 99 were identified in the MN map. Large numbers of NBS and PK profiling markers were found in clusters across different linkage groups, with the PK profiling markers more evenly distributed. The location of markers throughout the genetic maps and the composition of marker clusters indicate that NBS- and PK-based markers cover partly complementary regions of oat genomes. Markers of the different classes obtained were found associated with the two resistance loci, PcA and R-284B-2, mapped on Asw, and with five out of eight QTLs for partial resistance in the MN map. 53 RGA-RFLPs and 187 NBS/PK profiling markers were also mapped on the hexaploid map A. byzantina cv. Kanota × A. sativa cv. Ogle. Significant co-localization was seen between the RGA markers in the KO map and other markers closely linked to resistance loci, such as those for P. coronata and barley yellow dwarf virus (Bydv) that were previously mapped in other segregating populations.

The National Map Pilot Projects

USGS Publications Warehouse

,

2002-01-01

The U.S. Geological Survey (USGS) is developing The National Map to be a seamless, continuously maintained, and nationally consistent set of online, public domain, geographic base information. The National Map will serve as a foundation for integrating, sharing, and using other government and private sector data easily and consistently.

Topic Maps e-Learning Portal Development

ERIC Educational Resources Information Center

Olsevicova, Kamila

2006-01-01

Topic Maps, ISO/IEC 13250 standard, are designed to facilitate the organization and navigation of large collections of information objects by creating meta-level perspectives of their underlying concepts and relationships. The underlying structure of concepts and relations is expressed by domain ontologies. The Topics Maps technology can become…

Mapping of interaction domains between human repair proteins ERCC1 and XPF.

PubMed

de Laat, W L; Sijbers, A M; Odijk, H; Jaspers, N G; Hoeijmakers, J H

1998-09-15

ERCC1-XPF is a heterodimeric protein complexinvolved in nucleotide excision repair and recombinational processes. Like its homologous complex in Saccharomyces cerevisiae , Rad10-Rad1, it acts as a structure-specific DNA endonuclease, cleaving at duplex-single-stranded DNA junctions. In repair, ERCC1-XPF and Rad10-Rad1 make an incision on the the 5'-side of the lesion. No humans with a defect in the ERCC1 subunit of this protein complex have been identified and ERCC1-deficient mice suffer from severe developmental problems and signs of premature aging on top of a repair-deficient phenotype. Xeroderma pigmentosum group F patients carry mutations in the XPF subunit and generally show the clinical symptoms of mild DNA repair deficiency. All XP-F patients examined demonstrate reduced levels of XPF and ERCC1 protein, suggesting that proper complex formation is required for stability of the two proteins. To better understand the molecular and clinical consequences of mutations in the ERCC1-XPF complex, we decided to map the interaction domains between the two subunits. The XPF-binding domain comprises C-terminal residues 224-297 of ERCC1. Intriguingly, this domain resides outside the region of homology with its yeast Rad10 counterpart. The ERCC1-binding domain in XPF maps to C-terminal residues 814-905. ERCC1-XPF complex formation is established by a direct interaction between these two binding domains. A mutation from an XP-F patient that alters the ERCC1-binding domain in XPF indeed affects complex formation with ERCC1.

Mapping of interaction domains between human repair proteins ERCC1 and XPF.

PubMed Central

de Laat, W L; Sijbers, A M; Odijk, H; Jaspers, N G; Hoeijmakers, J H

1998-01-01

ERCC1-XPF is a heterodimeric protein complexinvolved in nucleotide excision repair and recombinational processes. Like its homologous complex in Saccharomyces cerevisiae , Rad10-Rad1, it acts as a structure-specific DNA endonuclease, cleaving at duplex-single-stranded DNA junctions. In repair, ERCC1-XPF and Rad10-Rad1 make an incision on the the 5'-side of the lesion. No humans with a defect in the ERCC1 subunit of this protein complex have been identified and ERCC1-deficient mice suffer from severe developmental problems and signs of premature aging on top of a repair-deficient phenotype. Xeroderma pigmentosum group F patients carry mutations in the XPF subunit and generally show the clinical symptoms of mild DNA repair deficiency. All XP-F patients examined demonstrate reduced levels of XPF and ERCC1 protein, suggesting that proper complex formation is required for stability of the two proteins. To better understand the molecular and clinical consequences of mutations in the ERCC1-XPF complex, we decided to map the interaction domains between the two subunits. The XPF-binding domain comprises C-terminal residues 224-297 of ERCC1. Intriguingly, this domain resides outside the region of homology with its yeast Rad10 counterpart. The ERCC1-binding domain in XPF maps to C-terminal residues 814-905. ERCC1-XPF complex formation is established by a direct interaction between these two binding domains. A mutation from an XP-F patient that alters the ERCC1-binding domain in XPF indeed affects complex formation with ERCC1. PMID:9722633

Preclinical evaluation of spatial frequency domain-enabled wide-field quantitative imaging for enhanced glioma resection

NASA Astrophysics Data System (ADS)

Sibai, Mira; Fisher, Carl; Veilleux, Israel; Elliott, Jonathan T.; Leblond, Frederic; Roberts, David W.; Wilson, Brian C.

2017-07-01

5-Aminolevelunic acid-induced protoporphyrin IX (PpIX) fluorescence-guided resection (FGR) enables maximum safe resection of glioma by providing real-time tumor contrast. However, the subjective visual assessment and the variable intrinsic optical attenuation of tissue limit this technique to reliably delineating only high-grade tumors that display strong fluorescence. We have previously shown, using a fiber-optic probe, that quantitative assessment using noninvasive point spectroscopic measurements of the absolute PpIX concentration in tissue further improves the accuracy of FGR, extending it to surgically curable low-grade glioma. More recently, we have shown that implementing spatial frequency domain imaging with a fluorescent-light transport model enables recovery of two-dimensional images of [PpIX], alleviating the need for time-consuming point sampling of the brain surface. We present first results of this technique modified for in vivo imaging on an RG2 rat brain tumor model. Despite the moderate errors in retrieving the absorption and reduced scattering coefficients in the subdiffusive regime of 14% and 19%, respectively, the recovered [PpIX] maps agree within 10% of the point [PpIX] values measured by the fiber-optic probe, validating its potential as an extension or an alternative to point sampling during glioma resection.

The Activation Domain of the Bovine Papillomavirus E2 Protein Mediates Association of DNA-Bound Dimers to form DNA Loops

NASA Astrophysics Data System (ADS)

Knight, Jonathan D.; Li, Rong; Botchan, Michael

1991-04-01

The E2 transactivator protein of bovine papillomavirus binds its specific DNA target sequence as a dimer. We have found that E2 dimers, performed in solution independent of DNA, exhibit substantial cooperativity of DNA binding as detected by both nitrocellulose filter retention and footprint analysis techniques. If the binding sites are widely spaced, E2 forms stable DNA loops visible by electron microscopy. When three widely separated binding sites reside on te DNA, E2 condenses the molecule into a bow-tie structure. This implies that each E2 dimer has at least two independent surfaces for multimerization. Two naturally occurring shorter forms of the protein, E2C and D8/E2, which function in vivo as repressors of transcription, do not form such loops. Thus, the looping function of E2 maps to the 161-amino acid activation domain. These results support the looping model of transcription activation by enhancers.

Parallel Solver for Diffuse Optical Tomography on Realistic Head Models With Scattering and Clear Regions.

PubMed

Placati, Silvio; Guermandi, Marco; Samore, Andrea; Scarselli, Eleonora Franchi; Guerrieri, Roberto

2016-09-01

Diffuse optical tomography is an imaging technique, based on evaluation of how light propagates within the human head to obtain the functional information about the brain. Precision in reconstructing such an optical properties map is highly affected by the accuracy of the light propagation model implemented, which needs to take into account the presence of clear and scattering tissues. We present a numerical solver based on the radiosity-diffusion model, integrating the anatomical information provided by a structural MRI. The solver is designed to run on parallel heterogeneous platforms based on multiple GPUs and CPUs. We demonstrate how the solver provides a 7 times speed-up over an isotropic-scattered parallel Monte Carlo engine based on a radiative transport equation for a domain composed of 2 million voxels, along with a significant improvement in accuracy. The speed-up greatly increases for larger domains, allowing us to compute the light distribution of a full human head ( ≈ 3 million voxels) in 116 s for the platform used.

On-line surface inspection using cylindrical lens-based spectral domain low-coherence interferometry.

PubMed

Tang, Dawei; Gao, Feng; Jiang, X

2014-08-20

We present a spectral domain low-coherence interferometry (SD-LCI) method that is effective for applications in on-line surface inspection because it can obtain a surface profile in a single shot. It has an advantage over existing spectral interferometry techniques by using cylindrical lenses as the objective lenses in a Michelson interferometric configuration to enable the measurement of long profiles. Combined with a modern high-speed CCD camera, general-purpose graphics processing unit, and multicore processors computing technology, fast measurement can be achieved. By translating the tested sample during the measurement procedure, real-time surface inspection was implemented, which is proved by the large-scale 3D surface measurement in this paper. ZEMAX software is used to simulate the SD-LCI system and analyze the alignment errors. Two step height surfaces were measured, and the captured interferograms were analyzed using a fast Fourier transform algorithm. Both 2D profile results and 3D surface maps closely align with the calibrated specifications given by the manufacturer.

SVD compression for magnetic resonance fingerprinting in the time domain.

PubMed

McGivney, Debra F; Pierre, Eric; Ma, Dan; Jiang, Yun; Saybasili, Haris; Gulani, Vikas; Griswold, Mark A

2014-12-01

Magnetic resonance (MR) fingerprinting is a technique for acquiring and processing MR data that simultaneously provides quantitative maps of different tissue parameters through a pattern recognition algorithm. A predefined dictionary models the possible signal evolutions simulated using the Bloch equations with different combinations of various MR parameters and pattern recognition is completed by computing the inner product between the observed signal and each of the predicted signals within the dictionary. Though this matching algorithm has been shown to accurately predict the MR parameters of interest, one desires a more efficient method to obtain the quantitative images. We propose to compress the dictionary using the singular value decomposition, which will provide a low-rank approximation. By compressing the size of the dictionary in the time domain, we are able to speed up the pattern recognition algorithm, by a factor of between 3.4-4.8, without sacrificing the high signal-to-noise ratio of the original scheme presented previously.

Design and Evaluation of a Bacterial Clinical Infectious Diseases Ontology

PubMed Central

Gordon, Claire L.; Pouch, Stephanie; Cowell, Lindsay G.; Boland, Mary Regina; Platt, Heather L.; Goldfain, Albert; Weng, Chunhua

2013-01-01

With antimicrobial resistance increasing worldwide, there is a great need to use automated antimicrobial decision support systems (ADSSs) to lower antimicrobial resistance rates by promoting appropriate antimicrobial use. However, they are infrequently used mostly because of their poor interoperability with different health information technologies. Ontologies can augment portable ADSSs by providing an explicit knowledge representation for biomedical entities and their relationships, helping to standardize and integrate heterogeneous data resources. We developed a bacterial clinical infectious diseases ontology (BCIDO) using Protégé-OWL. BCIDO defines a controlled terminology for clinical infectious diseases along with domain knowledge commonly used in hospital settings for clinical infectious disease treatment decision-making. BCIDO has 599 classes and 2355 object properties. Terms were imported from or mapped to Systematized Nomenclature of Medicine, Unified Medical Language System, RxNorm and National Center for Bitechnology Information Organismal Classification where possible. Domain expert evaluation using the “laddering” technique, ontology visualization, and clinical notes and scenarios, confirmed the correctness and potential usefulness of BCIDO. PMID:24551353

SVD Compression for Magnetic Resonance Fingerprinting in the Time Domain

PubMed Central

McGivney, Debra F.; Pierre, Eric; Ma, Dan; Jiang, Yun; Saybasili, Haris; Gulani, Vikas; Griswold, Mark A.

2016-01-01

Magnetic resonance fingerprinting is a technique for acquiring and processing MR data that simultaneously provides quantitative maps of different tissue parameters through a pattern recognition algorithm. A predefined dictionary models the possible signal evolutions simulated using the Bloch equations with different combinations of various MR parameters and pattern recognition is completed by computing the inner product between the observed signal and each of the predicted signals within the dictionary. Though this matching algorithm has been shown to accurately predict the MR parameters of interest, one desires a more efficient method to obtain the quantitative images. We propose to compress the dictionary using the singular value decomposition (SVD), which will provide a low-rank approximation. By compressing the size of the dictionary in the time domain, we are able to speed up the pattern recognition algorithm, by a factor of between 3.4-4.8, without sacrificing the high signal-to-noise ratio of the original scheme presented previously. PMID:25029380

Dark-field X-ray microscopy for multiscale structural characterization

NASA Astrophysics Data System (ADS)

Simons, H.; King, A.; Ludwig, W.; Detlefs, C.; Pantleon, W.; Schmidt, S.; Snigireva, I.; Snigirev, A.; Poulsen, H. F.

2015-01-01

Many physical and mechanical properties of crystalline materials depend strongly on their internal structure, which is typically organized into grains and domains on several length scales. Here we present dark-field X-ray microscopy; a non-destructive microscopy technique for the three-dimensional mapping of orientations and stresses on lengths scales from 100 nm to 1 mm within embedded sampling volumes. The technique, which allows ‘zooming’ in and out in both direct and angular space, is demonstrated by an annealing study of plastically deformed aluminium. Facilitating the direct study of the interactions between crystalline elements is a key step towards the formulation and validation of multiscale models that account for the entire heterogeneity of a material. Furthermore, dark-field X-ray microscopy is well suited to applied topics, where the structural evolution of internal nanoscale elements (for example, positioned at interfaces) is crucial to the performance and lifetime of macro-scale devices and components thereof.

Edge enhancement and noise suppression for infrared image based on feature analysis

NASA Astrophysics Data System (ADS)

Jiang, Meng

2018-06-01

Infrared images are often suffering from background noise, blurred edges, few details and low signal-to-noise ratios. To improve infrared image quality, it is essential to suppress noise and enhance edges simultaneously. To realize it in this paper, we propose a novel algorithm based on feature analysis in shearlet domain. Firstly, as one of multi-scale geometric analysis (MGA), we introduce the theory and superiority of shearlet transform. Secondly, after analyzing the defects of traditional thresholding technique to suppress noise, we propose a novel feature extraction distinguishing image structures from noise well and use it to improve the traditional thresholding technique. Thirdly, with computing the correlations between neighboring shearlet coefficients, the feature attribute maps identifying the weak detail and strong edges are completed to improve the generalized unsharped masking (GUM). At last, experiment results with infrared images captured in different scenes demonstrate that the proposed algorithm suppresses noise efficiently and enhances image edges adaptively.

Magnetic elements for switching magnetization magnetic force microscopy tips.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cambel, V.; Elias, P.; Gregusova, D.

2010-09-01

Using combination of micromagnetic calculations and magnetic force microscopy (MFM) imaging we find optimal parameters for novel magnetic tips suitable for switching magnetization MFM. Switching magnetization MFM is based on two-pass scanning atomic force microscopy with reversed tip magnetization between the scans. Within the technique the sum of the scanned data with reversed tip magnetization depicts local atomic forces, while their difference maps the local magnetic forces. Here we propose the design and calculate the magnetic properties of tips suitable for this scanning probe technique. We find that for best performance the spin-polarized tips must exhibit low magnetic moment, lowmore » switching fields, and single-domain state at remanence. The switching field of such tips is calculated and optimum shape of the Permalloy elements for the tips is found. We show excellent correspondence between calculated and experimental results for Py elements.« less

Rule Mining Techniques to Predict Prokaryotic Metabolic Pathways.

PubMed

Saidi, Rabie; Boudellioua, Imane; Martin, Maria J; Solovyev, Victor

2017-01-01

It is becoming more evident that computational methods are needed for the identification and the mapping of pathways in new genomes. We introduce an automatic annotation system (ARBA4Path Association Rule-Based Annotator for Pathways) that utilizes rule mining techniques to predict metabolic pathways across wide range of prokaryotes. It was demonstrated that specific combinations of protein domains (recorded in our rules) strongly determine pathways in which proteins are involved and thus provide information that let us very accurately assign pathway membership (with precision of 0.999 and recall of 0.966) to proteins of a given prokaryotic taxon. Our system can be used to enhance the quality of automatically generated annotations as well as annotating proteins with unknown function. The prediction models are represented in the form of human-readable rules, and they can be used effectively to add absent pathway information to many proteins in UniProtKB/TrEMBL database.

Axial resolution improvement in spectral domain optical coherence tomography using a depth-adaptive maximum-a-posterior framework

NASA Astrophysics Data System (ADS)

Boroomand, Ameneh; Tan, Bingyao; Wong, Alexander; Bizheva, Kostadinka

2015-03-01

The axial resolution of Spectral Domain Optical Coherence Tomography (SD-OCT) images degrades with scanning depth due to the limited number of pixels and the pixel size of the camera, any aberrations in the spectrometer optics and wavelength dependent scattering and absorption in the imaged object [1]. Here we propose a novel algorithm which compensates for the blurring effect of these factors of the depth-dependent axial Point Spread Function (PSF) in SDOCT images. The proposed method is based on a Maximum A Posteriori (MAP) reconstruction framework which takes advantage of a Stochastic Fully Connected Conditional Random Field (SFCRF) model. The aim is to compensate for the depth-dependent axial blur in SD-OCT images and simultaneously suppress the speckle noise which is inherent to all OCT images. Applying the proposed depth-dependent axial resolution enhancement technique to an OCT image of cucumber considerably improved the axial resolution of the image especially at higher imaging depths and allowed for better visualization of cellular membrane and nuclei. Comparing the result of our proposed method with the conventional Lucy-Richardson deconvolution algorithm clearly demonstrates the efficiency of our proposed technique in better visualization and preservation of fine details and structures in the imaged sample, as well as better speckle noise suppression. This illustrates the potential usefulness of our proposed technique as a suitable replacement for the hardware approaches which are often very costly and complicated.

Digital Mapping Techniques '11–12 workshop proceedings

USGS Publications Warehouse

Soller, David R.

2014-01-01

At these meetings, oral and poster presentations and special discussion sessions emphasized: (1) methods for creating and publishing map products (here, "publishing" includes Web-based release); (2) field data capture software and techniques, including the use of LiDAR; (3) digital cartographic techniques; (4) migration of digital maps into ArcGIS Geodatabase formats; (5) analytical GIS techniques; and (6) continued development of the National Geologic Map Database.

Added value products for imaging remote sensing by processing actual GNSS reflectometry delay doppler maps

NASA Astrophysics Data System (ADS)

Schiavulli, Domenico; Frappart, Frédéric; Ramilien, Guillaume; Darrozes, José; Nunziata, Ferdinando; Migliaccio, Maurizio

2016-04-01

Global Navigation Satellite System Reflectometry (GNSS-R) is an innovative and promising tool for remote sensing. It is based on the exploitation of GNSS signals reflected off Earth's surface as signals of opportunity to infer geophysical information of the reflecting surface. The main advantages of GNSS-R with respect dedicated sensors are: the unprecedented spatial-temporal coverage due to the availability of a great amount of transmitting satellite, e.g. GPS, Galileo, Glonass, etc…, long term GNSS mission life and cost effectiveness. In fact only a simple receiver is needed. In the last years several works demonstrated the meaningful of this technique in several Earth Observation applications. All these applications presented results obtained by using a receiver mounted on an aircraft or on a fixed platform. Moreover, space borne missions have been launched or are planned: UK-DMC, TechDemoSat-1 (TDS-1), NASA CYGNSS, Geros ISS. Practically, GNSS-R can be seen as a bistatic radar system where the GNSS satellites continuously transmit the L-band all-weather night-and-day signals that are reflected off a surface, called Glistening Zone (GZ), and a receiver measures the scattered microwave signals in terms of Delay-Doppler maps (DDMs) or delay waveforms. These two products have been widely studied in the literature to extract compact parameters for different remote sensing applications. However, products measured in the Delay Doppler (DD) domain are not able to provide any spatial information of the scattering scene. This could represent a drawback for applications related to imaging remote sensing, e.g. target detection, sea/land and sea/ice transition, oil spill detection, etc…. To overcome these limitations some deconvolution techniques have been proposed in the state of the art aiming at the reconstruction of a radar image of the observed scene by processing the measured DDMs. These techniques have been tested on DDMs related to simulated marine scenario including areas with different wind speed, oil spill, non-homogeneous area and cyclone. In this work a deconvolution technique based on the 2-D Truncated Singular Value Decomposition (TSVD) approach is used to process, for the first time, a real DDM measured by the TDS-1 mission to generate a radar image of the observed scene. The considered DDMs are related to marine scenario including non-homogenous area, i.e. sea/land and sea/ice transition. These non-homogeneous area provide a strong scattering contribution in the DD domain but it is not possible to extract any other information by analyzing the DDM. In the other hand, after the 2-D TSVD technique application a radar image of the observed scenario is provided where the transition between sea and non-homogeneous elements is reconstructed and well located in the spatial domain. Finally, in this work we demonstrate the soundness of the proposed approach able to provide an added value product for imaging remote sensing to improve/complement dedicated sensors.

Understanding disordered systems through numerical simulation and algorithm development

NASA Astrophysics Data System (ADS)

Sweeney, Sean Michael

Disordered systems arise in many physical contexts. Not all matter is uniform, and impurities or heterogeneities can be modeled by fixed random disorder. Numerous complex networks also possess fixed disorder, leading to applications in transportation systems, telecommunications, social networks, and epidemic modeling, to name a few. Due to their random nature and power law critical behavior, disordered systems are difficult to study analytically. Numerical simulation can help overcome this hurdle by allowing for the rapid computation of system states. In order to get precise statistics and extrapolate to the thermodynamic limit, large systems must be studied over many realizations. Thus, innovative algorithm development is essential in order reduce memory or running time requirements of simulations. This thesis presents a review of disordered systems, as well as a thorough study of two particular systems through numerical simulation, algorithm development and optimization, and careful statistical analysis of scaling properties. Chapter 1 provides a thorough overview of disordered systems, the history of their study in the physics community, and the development of techniques used to study them. Topics of quenched disorder, phase transitions, the renormalization group, criticality, and scale invariance are discussed. Several prominent models of disordered systems are also explained. Lastly, analysis techniques used in studying disordered systems are covered. In Chapter 2, minimal spanning trees on critical percolation clusters are studied, motivated in part by an analytic perturbation expansion by Jackson and Read that I check against numerical calculations. This system has a direct mapping to the ground state of the strongly disordered spin glass. We compute the path length fractal dimension of these trees in dimensions d = {2, 3, 4, 5} and find our results to be compatible with the analytic results suggested by Jackson and Read. In Chapter 3, the random bond Ising ferromagnet is studied, which is especially useful since it serves as a prototype for more complicated disordered systems such as the random field Ising model and spin glasses. We investigate the effect that changing boundary spins has on the locations of domain walls in the interior of the random ferromagnet system. We provide an analytic proof that ground state domain walls in the two dimensional system are decomposable, and we map these domain walls to a shortest paths problem. By implementing a multiple-source shortest paths algorithm developed by Philip Klein, we are able to efficiently probe domain wall locations for all possible configurations of boundary spins. We consider lattices with uncorrelated dis- order, as well as disorder that is spatially correlated according to a power law. We present numerical results for the scaling exponent governing the probability that a domain wall can be induced that passes through a particular location in the system's interior, and we compare these results to previous results on the directed polymer problem.

Linking of the quality of life in neurological disorders (Neuro-QoL) to the international classification of functioning, disability and health.

PubMed

Wong, Alex W K; Lau, Stephen C L; Cella, David; Lai, Jin-Shei; Xie, Guanli; Chen, Lidian; Chan, Chetwyn C H; Heinemann, Allen W

2017-09-01

The quality of life in neurological disorders (Neuro-QoL) is a U.S. National Institutes of Health initiative that produced a set of self-report measures of physical, mental, and social health experienced by adults or children who have a neurological condition or disorder. To describe the content of the Neuro-QoL at the item level using the World Health Organization's international classification of functioning, disability and health (ICF). We assessed the Neuro-QoL for its content coverage of functioning and disability relative to each of the four ICF domains (i.e., body functions, body structures, activities and participation, and environment). We used second-level ICF three-digit codes to classify items into categories within each ICF domain and computed the percentage of categories within each ICF domain that were represented in the Neuro-QoL items. All items of Neuro-QoL could be mapped to the ICF categories at the second-level classification codes. The activities and participation domain and the mental functions category of the body functions domain were the areas most often represented by Neuro-QoL. Neuro-QoL provides limited coverage of the environmental factors and body structure domains. Neuro-QoL measures map well to the ICF. The Neuro-QoL-ICF-mapped items provide a blueprint for users to select appropriate measures in ICF-based measurement applications.

MEG/EEG Source Reconstruction, Statistical Evaluation, and Visualization with NUTMEG

PubMed Central

Dalal, Sarang S.; Zumer, Johanna M.; Guggisberg, Adrian G.; Trumpis, Michael; Wong, Daniel D. E.; Sekihara, Kensuke; Nagarajan, Srikantan S.

2011-01-01

NUTMEG is a source analysis toolbox geared towards cognitive neuroscience researchers using MEG and EEG, including intracranial recordings. Evoked and unaveraged data can be imported to the toolbox for source analysis in either the time or time-frequency domains. NUTMEG offers several variants of adaptive beamformers, probabilistic reconstruction algorithms, as well as minimum-norm techniques to generate functional maps of spatiotemporal neural source activity. Lead fields can be calculated from single and overlapping sphere head models or imported from other software. Group averages and statistics can be calculated as well. In addition to data analysis tools, NUTMEG provides a unique and intuitive graphical interface for visualization of results. Source analyses can be superimposed onto a structural MRI or headshape to provide a convenient visual correspondence to anatomy. These results can also be navigated interactively, with the spatial maps and source time series or spectrogram linked accordingly. Animations can be generated to view the evolution of neural activity over time. NUTMEG can also display brain renderings and perform spatial normalization of functional maps using SPM's engine. As a MATLAB package, the end user may easily link with other toolboxes or add customized functions. PMID:21437174

MEG/EEG source reconstruction, statistical evaluation, and visualization with NUTMEG.

PubMed

Dalal, Sarang S; Zumer, Johanna M; Guggisberg, Adrian G; Trumpis, Michael; Wong, Daniel D E; Sekihara, Kensuke; Nagarajan, Srikantan S

2011-01-01

NUTMEG is a source analysis toolbox geared towards cognitive neuroscience researchers using MEG and EEG, including intracranial recordings. Evoked and unaveraged data can be imported to the toolbox for source analysis in either the time or time-frequency domains. NUTMEG offers several variants of adaptive beamformers, probabilistic reconstruction algorithms, as well as minimum-norm techniques to generate functional maps of spatiotemporal neural source activity. Lead fields can be calculated from single and overlapping sphere head models or imported from other software. Group averages and statistics can be calculated as well. In addition to data analysis tools, NUTMEG provides a unique and intuitive graphical interface for visualization of results. Source analyses can be superimposed onto a structural MRI or headshape to provide a convenient visual correspondence to anatomy. These results can also be navigated interactively, with the spatial maps and source time series or spectrogram linked accordingly. Animations can be generated to view the evolution of neural activity over time. NUTMEG can also display brain renderings and perform spatial normalization of functional maps using SPM's engine. As a MATLAB package, the end user may easily link with other toolboxes or add customized functions.

Quantitative Susceptibility Mapping by Inversion of a Perturbation Field Model: Correlation with Brain Iron in Normal Aging

PubMed Central

Poynton, Clare; Jenkinson, Mark; Adalsteinsson, Elfar; Sullivan, Edith V.; Pfefferbaum, Adolf; Wells, William

2015-01-01

There is increasing evidence that iron deposition occurs in specific regions of the brain in normal aging and neurodegenerative disorders such as Parkinson's, Huntington's, and Alzheimer's disease. Iron deposition changes the magnetic susceptibility of tissue, which alters the MR signal phase, and allows estimation of susceptibility differences using quantitative susceptibility mapping (QSM). We present a method for quantifying susceptibility by inversion of a perturbation model, or ‘QSIP’. The perturbation model relates phase to susceptibility using a kernel calculated in the spatial domain, in contrast to previous Fourier-based techniques. A tissue/air susceptibility atlas is used to estimate B0 inhomogeneity. QSIP estimates in young and elderly subjects are compared to postmortem iron estimates, maps of the Field-Dependent Relaxation Rate Increase (FDRI), and the L1-QSM method. Results for both groups showed excellent agreement with published postmortem data and in-vivo FDRI: statistically significant Spearman correlations ranging from Rho = 0.905 to Rho = 1.00 were obtained. QSIP also showed improvement over FDRI and L1-QSM: reduced variance in susceptibility estimates and statistically significant group differences were detected in striatal and brainstem nuclei, consistent with age-dependent iron accumulation in these regions. PMID:25248179

Application of diffusion maps to identify human factors of self-reported anomalies in aviation.

PubMed

Andrzejczak, Chris; Karwowski, Waldemar; Mikusinski, Piotr

2012-01-01

A study investigating what factors are present leading to pilots submitting voluntary anomaly reports regarding their flight performance was conducted. Diffusion Maps (DM) were selected as the method of choice for performing dimensionality reduction on text records for this study. Diffusion Maps have seen successful use in other domains such as image classification and pattern recognition. High-dimensionality data in the form of narrative text reports from the NASA Aviation Safety Reporting System (ASRS) were clustered and categorized by way of dimensionality reduction. Supervised analyses were performed to create a baseline document clustering system. Dimensionality reduction techniques identified concepts or keywords within records, and allowed the creation of a framework for an unsupervised document classification system. Results from the unsupervised clustering algorithm performed similarly to the supervised methods outlined in the study. The dimensionality reduction was performed on 100 of the most commonly occurring words within 126,000 text records describing commercial aviation incidents. This study demonstrates that unsupervised machine clustering and organization of incident reports is possible based on unbiased inputs. Findings from this study reinforced traditional views on what factors contribute to civil aviation anomalies, however, new associations between previously unrelated factors and conditions were also found.

Hyperspectral remote sensing applied to mineral exploration in southern Peru: A multiple data integration approach in the Chapi Chiara gold prospect

NASA Astrophysics Data System (ADS)

Carrino, Thais Andressa; Crósta, Alvaro Penteado; Toledo, Catarina Labouré Bemfica; Silva, Adalene Moreira

2018-02-01

Remote sensing is a strategic key tool for mineral exploration, due to its capacity of detecting hydrothermal alteration minerals or alteration mineral zones associated with different types of mineralization systems. A case study of an epithermal system located in southern Peru is presented, aimed at the characterization of mineral assemblies for discriminating potential high sulfidation epithermal targets, using hyperspectral imagery integrated with petrography, XRD and magnetic data. HyMap images were processed using the Mixture Tuned Matched Filtering (MTMF) technique for producing alteration map in the Chapi Chiara epithermal gold prospect. Extensive areas marked by advanced argillic alteration (alunite-kaolinite-dickite ± topaz) were mapped in detail, as well as limited argillic (illite-smectite) and propylitic (chlorite spectral domain) alteration. The magmatic-hydrothermal processes responsible for the formation of hypogene minerals were also related to the destruction of ferrimagnetic minerals (e.g., magnetite) of host rocks such as andesite, and the remobilization/formation of paramagnetic Fe-Ti oxides (e.g., rutile, anatase). The large alteration zones of advanced argillic alteration are controlled by structures related to a regional NW-SE trend, and also by local NE-SW and ENE-WSW ones.

Numerical modeling of crystal growth in Bridgman device

NASA Astrophysics Data System (ADS)

Vompe, Dmitry Aleksandrovich

1997-12-01

The standard model for the growth of a crystal from a pure substance or diluted binary mixture contains transport equations for heat and phase change conditions at the solidification front. A numerical method is constructed for simulations of crystal growth in a vertical Bridgman device. The method is based on a boundary fitting technique in which melted and solidified regions are mapped onto a fixed rectangular logical domain. The Alternating Directions scheme (ADI) is used to treat the diffusive terms implicitly, with explicit methods are used for the remaining terms in the mapped temperature equations with variable coefficients. The nonlinear equation for the solid/liquid interface motion is solved by the modified Euler technique. Results obtained from the calculations have been used to study the influence of various boundary conditions imposed on the sidewalls and the top and bottom of the ampoule. Conditions are identified that lead to a steadily growing crystal and results are compared with an asymptotic one- dimensional model. Criteria based on ampoule length and boundary conditions being derived and compared with a previously developed one-dimensional model. Various cases have been considered to determine conditions for maintaining a nearly flat interface. It was found that the interface amplitude can be decreased by a factor of 100 (even 1,000) by optimizing temperature boundary conditions.

Multifrequency spectrum analysis using fully digital G Mode-Kelvin probe force microscopy.

PubMed

Collins, Liam; Belianinov, Alex; Somnath, Suhas; Rodriguez, Brian J; Balke, Nina; Kalinin, Sergei V; Jesse, Stephen

2016-03-11

Since its inception over two decades ago, Kelvin probe force microscopy (KPFM) has become the standard technique for characterizing electrostatic, electrochemical and electronic properties at the nanoscale. In this work, we present a purely digital, software-based approach to KPFM utilizing big data acquisition and analysis methods. General mode (G-Mode) KPFM works by capturing the entire photodetector data stream, typically at the sampling rate limit, followed by subsequent de-noising, analysis and compression of the cantilever response. We demonstrate that the G-Mode approach allows simultaneous multi-harmonic detection, combined with on-the-fly transfer function correction-required for quantitative CPD mapping. The KPFM approach outlined in this work significantly simplifies the technique by avoiding cumbersome instrumentation optimization steps (i.e. lock in parameters, feedback gains etc), while also retaining the flexibility to be implemented on any atomic force microscopy platform. We demonstrate the added advantages of G-Mode KPFM by allowing simultaneous mapping of CPD and capacitance gradient (C') channels as well as increased flexibility in data exploration across frequency, time, space, and noise domains. G-Mode KPFM is particularly suitable for characterizing voltage sensitive materials or for operation in conductive electrolytes, and will be useful for probing electrodynamics in photovoltaics, liquids and ionic conductors.

Skin Parameter Map Retrieval from a Dedicated Multispectral Imaging System Applied to Dermatology/Cosmetology

PubMed Central

2013-01-01

In vivo quantitative assessment of skin lesions is an important step in the evaluation of skin condition. An objective measurement device can help as a valuable tool for skin analysis. We propose an explorative new multispectral camera specifically developed for dermatology/cosmetology applications. The multispectral imaging system provides images of skin reflectance at different wavebands covering visible and near-infrared domain. It is coupled with a neural network-based algorithm for the reconstruction of reflectance cube of cutaneous data. This cube contains only skin optical reflectance spectrum in each pixel of the bidimensional spatial information. The reflectance cube is analyzed by an algorithm based on a Kubelka-Munk model combined with evolutionary algorithm. The technique allows quantitative measure of cutaneous tissue and retrieves five skin parameter maps: melanin concentration, epidermis/dermis thickness, haemoglobin concentration, and the oxygenated hemoglobin. The results retrieved on healthy participants by the algorithm are in good accordance with the data from the literature. The usefulness of the developed technique was proved during two experiments: a clinical study based on vitiligo and melasma skin lesions and a skin oxygenation experiment (induced ischemia) with healthy participant where normal tissues are recorded at normal state and when temporary ischemia is induced. PMID:24159326

Multifrequency spectrum analysis using fully digital G Mode-Kelvin probe force microscopy

DOE PAGES

Collins, Liam F.; Jesse, Stephen; Belianinov, Alex; ...

2016-02-11

Since its inception over two decades ago, Kelvin probe force microscopy (KPFM) has become the standard technique for characterizing electrostatic, electrochemical and electronic properties at the nanoscale. In this work, we present a purely digital, software-based approach to KPFM utilizing big data acquisition and analysis methods. General Mode (G-Mode) KPFM, works by capturing the entire photodetector data stream, typically at the sampling rate limit, followed by subsequent de-noising, analysis and compression of the cantilever response. We demonstrate that the G-Mode approach allows simultaneous multi-harmonic detection, combined with on-the-fly transfer function correction required for quantitative CPD mapping. The KPFM approach outlinedmore » in this work significantly simplifies the technique by avoiding cumbersome instrumentation optimization steps (i.e. lock in parameters, feedback gains etc.), while also retaining the flexibility to be implemented on any atomic force microscopy platform. We demonstrate the added advantages of G-Mode KPFM by allowing simultaneous mapping of CPD and capacitance gradient (C') channels as well as increased flexibility in data exploration across frequency, time, space, and noise domains. As a result, G-Mode KPFM is particularly suitable for characterizing voltage sensitive materials or for operation in conductive electrolytes, and will be useful for probing electrodynamics in photovoltaics, liquids and ionic conductors.« less

Care maps for children with medical complexity.

PubMed

Adams, Sherri; Nicholas, David; Mahant, Sanjay; Weiser, Natalie; Kanani, Ronik; Boydell, Katherine; Cohen, Eyal

2017-12-01

Children with medical complexity require multiple providers and services to keep them well and at home. A care map is a patient/family-created diagram that pictorially maps out this complex web of services. This study explored what care maps mean for families and healthcare providers to inform potential for clinical use. Parents (n=15) created care maps (hand drawn n=10 and computer-generated n=5) and participated in semi-structured interviews about the process of developing care maps and their perceived impact. Healthcare providers (n=30) reviewed the parent-created care maps and participated in semi-structured interviews. Data were analysed for themes and emerging theory using a grounded theory analytical approach. Data analysis revealed 13 overarching themes that were further categorized into three domains: features (characteristics of care maps), functions (what care maps do), and emerging outcomes (benefits of care map use). These domains further informed a definition and a theoretical model of how care maps work. Our findings suggest that care maps may be a way of supporting patient- and family-centred care by graphically identifying and integrating experiences of the family as well as priorities for moving forward. Care maps were endorsed as a useful tool by families and providers. They help healthcare providers better understand parental priorities for care. Parents can create care maps to demonstrate the complex burden of care. They are a unique visual way to incorporate narrative medicine into practice. © 2017 Mac Keith Press.

Positive visualization of implanted devices with susceptibility gradient mapping using the original resolution.

PubMed

Varma, Gopal; Clough, Rachel E; Acher, Peter; Sénégas, Julien; Dahnke, Hannes; Keevil, Stephen F; Schaeffter, Tobias

2011-05-01

In magnetic resonance imaging, implantable devices are usually visualized with a negative contrast. Recently, positive contrast techniques have been proposed, such as susceptibility gradient mapping (SGM). However, SGM reduces the spatial resolution making positive visualization of small structures difficult. Here, a development of SGM using the original resolution (SUMO) is presented. For this, a filter is applied in k-space and the signal amplitude is analyzed in the image domain to determine quantitatively the susceptibility gradient for each pixel. It is shown in simulations and experiments that SUMO results in a better visualization of small structures in comparison to SGM. SUMO is applied to patient datasets for visualization of stent and prostate brachytherapy seeds. In addition, SUMO also provides quantitative information about the number of prostate brachytherapy seeds. The method might be extended to application for visualization of other interventional devices, and, like SGM, it might also be used to visualize magnetically labelled cells. Copyright © 2010 Wiley-Liss, Inc.

Effortless assignment with 4D covariance sequential correlation maps.

PubMed

Harden, Bradley J; Mishra, Subrata H; Frueh, Dominique P

2015-11-01

Traditional Nuclear Magnetic Resonance (NMR) assignment procedures for proteins rely on preliminary peak-picking to identify and label NMR signals. However, such an approach has severe limitations when signals are erroneously labeled or completely neglected. The consequences are especially grave for proteins with substantial peak overlap, and mistakes can often thwart entire projects. To overcome these limitations, we previously introduced an assignment technique that bypasses traditional pick peaking altogether. Covariance Sequential Correlation Maps (COSCOMs) transform the indirect connectivity information provided by multiple 3D backbone spectra into direct (H, N) to (H, N) correlations. Here, we present an updated method that utilizes a single four-dimensional spectrum rather than a suite of three-dimensional spectra. We demonstrate the advantages of 4D-COSCOMs relative to their 3D counterparts. We introduce improvements accelerating their calculation. We discuss practical considerations affecting their quality. And finally we showcase their utility in the context of a 52 kDa cyclization domain from a non-ribosomal peptide synthetase. Copyright © 2015 Elsevier Inc. All rights reserved.

Effortless assignment with 4D covariance sequential correlation maps

NASA Astrophysics Data System (ADS)

Harden, Bradley J.; Mishra, Subrata H.; Frueh, Dominique P.

2015-11-01

Traditional Nuclear Magnetic Resonance (NMR) assignment procedures for proteins rely on preliminary peak-picking to identify and label NMR signals. However, such an approach has severe limitations when signals are erroneously labeled or completely neglected. The consequences are especially grave for proteins with substantial peak overlap, and mistakes can often thwart entire projects. To overcome these limitations, we previously introduced an assignment technique that bypasses traditional pick peaking altogether. Covariance Sequential Correlation Maps (COSCOMs) transform the indirect connectivity information provided by multiple 3D backbone spectra into direct (H, N) to (H, N) correlations. Here, we present an updated method that utilizes a single four-dimensional spectrum rather than a suite of three-dimensional spectra. We demonstrate the advantages of 4D-COSCOMs relative to their 3D counterparts. We introduce improvements accelerating their calculation. We discuss practical considerations affecting their quality. And finally we showcase their utility in the context of a 52 kDa cyclization domain from a non-ribosomal peptide synthetase.

[Detection of cerebral hypoperfusion using single photon emission computed tomography image analysis and statistical parametric mapping in patients with Parkinson's disease or progressive supranuclear palsy].

PubMed

Harada, Kengo; Saeki, Hiroshi; Matsuya, Eiji; Okita, Izumi

2013-11-01

We carried out differential diagnosis of brain blood flow images using single-photon emission computed tomography (SPECT) for patients with Parkinson's disease (PD) or progressive supranuclear paralysis (PSP) using statistical parametric mapping (SPM) and to whom we had applied anatomical standardization. We studied two groups and compared brain blood flow images using SPECT (N-isopropyl-4-iodoamphetamine [(123)I] hydrochloride injection, 222 MGq dosage i.v.). A total of 27 patients were studied using SPM: 18 with PD and 9 with PSP; humming bird sign on MRI was from moderate to medium. The decline of brain bloodstream in the PSP group was more notable in the midbrain, near the domain where the humming bird sign was observable, than in the PD group. The observable differences in brain bloodstream decline in the midbrain of PSP and PD patients suggest the potential usefulness of this technique's clinical application to distinction diagnosis.

Speech Enhancement, Gain, and Noise Spectrum Adaptation Using Approximate Bayesian Estimation

PubMed Central

Hao, Jiucang; Attias, Hagai; Nagarajan, Srikantan; Lee, Te-Won; Sejnowski, Terrence J.

2010-01-01

This paper presents a new approximate Bayesian estimator for enhancing a noisy speech signal. The speech model is assumed to be a Gaussian mixture model (GMM) in the log-spectral domain. This is in contrast to most current models in frequency domain. Exact signal estimation is a computationally intractable problem. We derive three approximations to enhance the efficiency of signal estimation. The Gaussian approximation transforms the log-spectral domain GMM into the frequency domain using minimal Kullback–Leiber (KL)-divergency criterion. The frequency domain Laplace method computes the maximum a posteriori (MAP) estimator for the spectral amplitude. Correspondingly, the log-spectral domain Laplace method computes the MAP estimator for the log-spectral amplitude. Further, the gain and noise spectrum adaptation are implemented using the expectation–maximization (EM) algorithm within the GMM under Gaussian approximation. The proposed algorithms are evaluated by applying them to enhance the speeches corrupted by the speech-shaped noise (SSN). The experimental results demonstrate that the proposed algorithms offer improved signal-to-noise ratio, lower word recognition error rate, and less spectral distortion. PMID:20428253

Exploring physics concepts among novice teachers through CMAP tools

NASA Astrophysics Data System (ADS)

Suprapto, N.; Suliyanah; Prahani, B. K.; Jauhariyah, M. N. R.; Admoko, S.

2018-03-01

Concept maps are graphical tools for organising, elaborating and representing knowledge. Through Cmap tools software, it can be explored the understanding and the hierarchical structuring of physics concepts among novice teachers. The software helps physics teachers indicated a physics context, focus questions, parking lots, cross-links, branching, hierarchy, and propositions. By using an exploratory quantitative study, a total 13-concept maps with different physics topics created by novice physics teachers were analysed. The main differences of scoring between lecturer and peer-teachers’ scoring were also illustrated. The study offered some implications, especially for physics educators to determine the hierarchical structure of the physics concepts, to construct a physics focus question, and to see how a concept in one domain of knowledge represented on the map is related to a concept in another domain shown on the map.

DNA Double-Strand Breaks Coupled with PARP1 and HNRNPA2B1 Binding Sites Flank Coordinately Expressed Domains in Human Chromosomes

PubMed Central

Fedoseeva, Daria M.; Sosin, Dmitri V.; Grachev, Sergei A.; Serebraykova, Marina V.; Romanenko, Svetlana A.; Vorobieva, Nadezhda V.; Kravatsky, Yuri V.

2013-01-01

Genome instability plays a key role in multiple biological processes and diseases, including cancer. Genome-wide mapping of DNA double-strand breaks (DSBs) is important for understanding both chromosomal architecture and specific chromosomal regions at DSBs. We developed a method for precise genome-wide mapping of blunt-ended DSBs in human chromosomes, and observed non-random fragmentation and DSB hot spots. These hot spots are scattered along chromosomes and delimit protected 50–250 kb DNA domains. We found that about 30% of the domains (denoted forum domains) possess coordinately expressed genes and that PARP1 and HNRNPA2B1 specifically bind DNA sequences at the forum domain termini. Thus, our data suggest a novel type of gene regulation: a coordinated transcription or silencing of gene clusters delimited by DSB hot spots as well as PARP1 and HNRNPa2B1 binding sites. PMID:23593027

An information sources map for Occupational and Environmental Medicine: guidance to network-based information through domain-specific indexing.

PubMed Central

Silverstein, S. M.; Miller, P. L.; Cullen, M. R.

1993-01-01

This paper describes a prototype information sources map (ISM), an on-line information source finder, for Occupational and Environmental Medicine (OEM). The OEM ISM was built as part of the Unified Medical Language System (UMLS) project of the National Library of Medicine. It allows a user to identify sources of on-line information appropriate to a specific OEM question, and connect to the sources. In the OEM ISM we explore a domain-specific method of indexing information source contents, and also a domain-specific user interface. The indexing represents a domain expert's opinion of the specificity of an information source in helping to answer specific types of domain questions. For each information source, an index field represents whether a source might provide useful information in an occupational, industrial, or environmental category. Additional fields represent the degree of specificity of a source in individual question types in each category. The paper discusses the development, design, and implementation of the prototype OEM ISM. PMID:8130548

Analyzing the Effects of Various Concept Mapping Techniques on Learning Achievement under Different Learning Styles

ERIC Educational Resources Information Center

Chiou, Chei-Chang; Lee, Li-Tze; Tien, Li-Chu; Wang, Yu-Min

2017-01-01

This study explored the effectiveness of different concept mapping techniques on the learning achievement of senior accounting students and whether achievements attained using various techniques are affected by different learning styles. The techniques are computer-assisted construct-by-self-concept mapping (CACSB), computer-assisted…

A stable downward continuation of airborne magnetic data: A case study for mineral prospectivity mapping in Central Iran

NASA Astrophysics Data System (ADS)

Abedi, Maysam; Gholami, Ali; Norouzi, Gholam-Hossain

2013-03-01

Previous studies have shown that a well-known multi-criteria decision making (MCDM) technique called Preference Ranking Organization METHod for Enrichment Evaluation (PROMETHEE II) to explore porphyry copper deposits can prioritize the ground-based exploratory evidential layers effectively. In this paper, the PROMETHEE II method is applied to airborne geophysical (potassium radiometry and magnetometry) data, geological layers (fault and host rock zones), and various extracted alteration layers from remote sensing images. The central Iranian volcanic-sedimentary belt is chosen for this study. A stable downward continuation method as an inverse problem in the Fourier domain using Tikhonov and edge-preserving regularizations is proposed to enhance magnetic data. Numerical analysis of synthetic models show that the reconstructed magnetic data at the ground surface exhibits significant enhancement compared to the airborne data. The reduced-to-pole (RTP) and the analytic signal filters are applied to the magnetic data to show better maps of the magnetic anomalies. Four remote sensing evidential layers including argillic, phyllic, propylitic and hydroxyl alterations are extracted from Advanced Spaceborne Thermal Emission and Reflection Radiometer (ASTER) images in order to map the altered areas associated with porphyry copper deposits. Principal component analysis (PCA) based on six Enhanced Thematic Mapper Plus (ETM+) images is implemented to map iron oxide layer. The final mineral prospectivity map based on desired geo-data set indicates adequately matching of high potential zones with previous working mines and copper deposits.

What are the 'active ingredients' of interventions targeting the public's engagement with antimicrobial resistance and how might they work?

PubMed

McParland, Joanna L; Williams, Lynn; Gozdzielewska, Lucyna; Young, Mairi; Smith, Fraser; MacDonald, Jennifer; Langdridge, Darren; Davis, Mark; Price, Lesley; Flowers, Paul

2018-05-27

Changing public awareness of antimicrobial resistance (AMR) represents a global public health priority. A systematic review of interventions that targeted public AMR awareness and associated behaviour was previously conducted. Here, we focus on identifying the active content of these interventions and explore potential mechanisms of action. The project took a novel approach to intervention mapping utilizing the following steps: (1) an exploration of explicit and tacit theory and theoretical constructs within the interventions using the Theoretical Domains Framework (TDFv2), (2) retrospective coding of behaviour change techniques (BCTs) using the BCT Taxonomy v1, and (3) an investigation of coherent links between the TDF domains and BCTs across the interventions. Of 20 studies included, only four reported an explicit theoretical basis to their intervention. However, TDF analysis revealed that nine of the 14 TDF domains were utilized, most commonly 'Knowledge' and 'Environmental context and resources'. The BCT analysis showed that all interventions contained at least one BCT, and 14 of 93 (15%) BCTs were coded, most commonly 'Information about health consequences', 'Credible source', and 'Instruction on how to perform the behaviour'. We identified nine relevant TDF domains and 14 BCTs used in these interventions. Only 15% of BCTs have been applied in AMR interventions thus providing a clear opportunity for the development of novel interventions in this context. This methodological approach provides a useful way of retrospectively mapping theoretical constructs and BCTs when reviewing studies that provide limited information on theory and intervention content. Statement of contribution What is already known on this subject? Evidence of the effectiveness of interventions that target the public to engage them with AMR is mixed; the public continue to show poor knowledge and misperceptions of AMR. Little is known about the common, active ingredients of AMR interventions targeting the public and information on explicit theoretical content is sparse. Information on the components of AMR public health interventions is urgently needed to enable the design of effective interventions to engage the public with AMR stewardship behaviour. What does this study add? The analysis shows very few studies reported any explicit theoretical basis to the interventions they described. Many interventions share common components, including core mechanisms of action and behaviour change techniques. The analysis suggests components of future interventions to engage the public with AMR. © 2018 The Authors. British Journal of Health Psychology published by John Wiley & Sons Ltd on behalf of British Psychological Society.

Color image encryption by using Yang-Gu mixture amplitude-phase retrieval algorithm in gyrator transform domain and two-dimensional Sine logistic modulation map

NASA Astrophysics Data System (ADS)

Sui, Liansheng; Liu, Benqing; Wang, Qiang; Li, Ye; Liang, Junli

2015-12-01

A color image encryption scheme is proposed based on Yang-Gu mixture amplitude-phase retrieval algorithm and two-coupled logistic map in gyrator transform domain. First, the color plaintext image is decomposed into red, green and blue components, which are scrambled individually by three random sequences generated by using the two-dimensional Sine logistic modulation map. Second, each scrambled component is encrypted into a real-valued function with stationary white noise distribution in the iterative amplitude-phase retrieval process in the gyrator transform domain, and then three obtained functions are considered as red, green and blue channels to form the color ciphertext image. Obviously, the ciphertext image is real-valued function and more convenient for storing and transmitting. In the encryption and decryption processes, the chaotic random phase mask generated based on logistic map is employed as the phase key, which means that only the initial values are used as private key and the cryptosystem has high convenience on key management. Meanwhile, the security of the cryptosystem is enhanced greatly because of high sensitivity of the private keys. Simulation results are presented to prove the security and robustness of the proposed scheme.

Gps-Denied Geo-Localisation Using Visual Odometry

NASA Astrophysics Data System (ADS)

Gupta, Ashish; Chang, Huan; Yilmaz, Alper

2016-06-01

The primary method for geo-localization is based on GPS which has issues of localization accuracy, power consumption, and unavailability. This paper proposes a novel approach to geo-localization in a GPS-denied environment for a mobile platform. Our approach has two principal components: public domain transport network data available in GIS databases or OpenStreetMap; and a trajectory of a mobile platform. This trajectory is estimated using visual odometry and 3D view geometry. The transport map information is abstracted as a graph data structure, where various types of roads are modelled as graph edges and typically intersections are modelled as graph nodes. A search for the trajectory in real time in the graph yields the geo-location of the mobile platform. Our approach uses a simple visual sensor and it has a low memory and computational footprint. In this paper, we demonstrate our method for trajectory estimation and provide examples of geolocalization using public-domain map data. With the rapid proliferation of visual sensors as part of automated driving technology and continuous growth in public domain map data, our approach has the potential to completely augment, or even supplant, GPS based navigation since it functions in all environments.

Improving semantic scene understanding using prior information

NASA Astrophysics Data System (ADS)

Laddha, Ankit; Hebert, Martial

2016-05-01

Perception for ground robot mobility requires automatic generation of descriptions of the robot's surroundings from sensor input (cameras, LADARs, etc.). Effective techniques for scene understanding have been developed, but they are generally purely bottom-up in that they rely entirely on classifying features from the input data based on learned models. In fact, perception systems for ground robots have a lot of information at their disposal from knowledge about the domain and the task. For example, a robot in urban environments might have access to approximate maps that can guide the scene interpretation process. In this paper, we explore practical ways to combine such prior information with state of the art scene understanding approaches.

A Mapping from the Human Factors Analysis and Classification System (DOD-HFACS) to the Domains of Human Systems Integration (HSI)

DTIC Science & Technology

2009-11-01

Equation Chapter 1 Section 1 A MAPPING FROM THE HUMAN FACTORS ANALYSIS AND CLASSIFICATION SYSTEM (DOD...OMB control number. 1. REPORT DATE NOV 2009 2. REPORT TYPE 3. DATES COVERED 4. TITLE AND SUBTITLE A Mapping from the Human Factors Analysis ...7 The Human Factors Analysis and Classification System .................................................. 7 Mapping of DoD

Photoluminescence Segmentation within Individual Hexagonal Monolayer Tungsten Disulfide Domains Grown by Chemical Vapor Deposition.

PubMed

Sheng, Yuewen; Wang, Xiaochen; Fujisawa, Kazunori; Ying, Siqi; Elias, Ana Laura; Lin, Zhong; Xu, Wenshuo; Zhou, Yingqiu; Korsunsky, Alexander M; Bhaskaran, Harish; Terrones, Mauricio; Warner, Jamie H

2017-05-03

We show that hexagonal domains of monolayer tungsten disulfide (WS 2 ) grown by chemical vapor deposition (CVD) with powder precursors can have discrete segmentation in their photoluminescence (PL) emission intensity, forming symmetric patterns with alternating bright and dark regions. Two-dimensional maps of the PL reveal significant reduction within the segments associated with the longest sides of the hexagonal domains. Analysis of the PL spectra shows differences in the exciton to trion ratio, indicating variations in the exciton recombination dynamics. Monolayers of WS 2 hexagonal islands transferred to new substrates still exhibit this PL segmentation, ruling out local strain in the regions as the dominant cause. High-power laser irradiation causes preferential degradation of the bright segments by sulfur removal, indicating the presence of a more defective region that is higher in oxidative reactivity. Atomic force microscopy (AFM) images of topography and amplitude modes show uniform thickness of the WS 2 domains and no signs of segmentation. However, AFM phase maps do show the same segmentation of the domain as the PL maps and indicate that it is caused by some kind of structural difference that we could not clearly identify. These results provide important insights into the spatially varying properties of these CVD-grown transition metal dichalcogenide materials, which may be important for their effective implementation in fast photo sensors and optical switches.

Competency Maps: an Effective Model to Integrate Professional Competencies Across a STEM Curriculum

NASA Astrophysics Data System (ADS)

Sánchez Carracedo, Fermín; Soler, Antonia; Martín, Carme; López, David; Ageno, Alicia; Cabré, Jose; Garcia, Jordi; Aranda, Joan; Gibert, Karina

2018-05-01

Curricula designed in the context of the European Higher Education Area need to be based on both domain-specific and professional competencies. Whereas universities have had extensive experience in developing students' domain-specific competencies, fostering professional competencies poses a new challenge we need to face. This paper presents a model to globally develop professional competencies in a STEM (science, technology, engineering, and mathematics) degree program, and assesses the results of its implementation after 4 years. The model is based on the use of competency maps, in which each competency is defined in terms of competency units. Each competency unit is described by a set of expected learning outcomes at three domain levels. This model allows careful analysis, revision, and iteration for an effective integration of professional competencies in domain-specific subjects. A global competency map is also designed, including all the professional competency learning outcomes to be achieved throughout the degree. This map becomes a useful tool for curriculum designers and coordinators. The results were obtained from four sources: (1) students' grades (classes graduated from 2013 to 2016, the first 4 years of the new Bachelor's Degree in Informatics Engineering at the Barcelona School of Informatics); (2) students' surveys (answered by students when they finished the degree); (3) the government employment survey, where former students evaluate their satisfaction of the received training in the light of their work experience; and (4) the Everis Foundation University-Enterprise Ranking, answered by over 2000 employers evaluating their satisfaction regarding their employees' university training, where the Barcelona School of Informatics scores first in the national ranking. The results show that competency maps are a good tool for developing professional competencies in a STEM degree.

Hot deformation constitutive equation and processing map of Alloy 690

NASA Astrophysics Data System (ADS)

Feng, Han; Zhang, Songchuang; Ma, Mingjuan; Song, Zhigang

The hot deformation behavior of alloy 690 was studied in the temperature range of 800-1300 C and strain rate range of 0.1-10 s-1 by hot compression tests in a Gleeble 1500+ thermal mechanical simulator. The results indicated that flow stress of alloy 690 is sensitive to deformation temperature and strain rate and peak stress increases with decreasing of temperature and increasing of strain rate. In addition, the hot deformation parameters of deformation activation were calculated and the apparent activation energy of this alloy is about 300 kJ/mol. The constitutive equation which can be used to relate peak stress to the absolute temperature and strain rate was obtained. It's further found that the processing maps exhibited two domains which are considered as the optimum windows for hot working. The microstructure observations of the specimens deformed in this domain showed the full dynamic recrystallization (DRX) structure. There was a flow instability domain in the processing map where hot working should be avoided.

Convergence of topological domain boundaries, insulators, and polytene interbands revealed by high-resolution mapping of chromatin contacts in the early Drosophila melanogaster embryo

PubMed Central

Stadler, Michael R; Haines, Jenna E

2017-01-01

High-throughput assays of three-dimensional interactions of chromosomes have shed considerable light on the structure of animal chromatin. Despite this progress, the precise physical nature of observed structures and the forces that govern their establishment remain poorly understood. Here we present high resolution Hi-C data from early Drosophila embryos. We demonstrate that boundaries between topological domains of various sizes map to DNA elements that resemble classical insulator elements: short genomic regions sensitive to DNase digestion that are strongly bound by known insulator proteins and are frequently located between divergent promoters. Further, we show a striking correspondence between these elements and the locations of mapped polytene interband regions. We believe it is likely this relationship between insulators, topological boundaries, and polytene interbands extends across the genome, and we therefore propose a model in which decompaction of boundary-insulator-interband regions drives the organization of interphase chromosomes by creating stable physical separation between adjacent domains. PMID:29148971

Multiple Antigenic Sites Are Involved in Blocking the Interaction of GII.4 Norovirus Capsid with ABH Histo-Blood Group Antigens

PubMed Central

Parra, Gabriel I.; Abente, Eugenio J.; Sandoval-Jaime, Carlos; Sosnovtsev, Stanislav V.; Bok, Karin

2012-01-01

Noroviruses are major etiological agents of acute viral gastroenteritis. In 2002, a GII.4 variant (Farmington Hills cluster) spread so rapidly in the human population that it predominated worldwide and displaced previous GII.4 strains. We developed and characterized a panel of six monoclonal antibodies (MAbs) directed against the capsid protein of a Farmington Hills-like GII.4 norovirus strain that was associated with a large hospital outbreak in Maryland in 2004. The six MAbs reacted with high titers against homologous virus-like particles (VLPs) by enzyme-linked immunoassay but did not react with denatured capsid protein in immunoblots. The expression and self-assembly of newly developed genogroup I/II chimeric VLPs showed that five MAbs bound to the GII.4 protruding (P) domain of the capsid protein, while one recognized the GII.4 shell (S) domain. Cross-competition assays and mutational analyses showed evidence for at least three distinct antigenic sites in the P domain and one in the S domain. MAbs that mapped to the P domain but not the S domain were able to block the interaction of VLPs with ABH histo-blood group antigens (HBGA), suggesting that multiple antigenic sites of the P domain are involved in HBGA blocking. Further analysis showed that two MAbs mapped to regions of the capsid that had been associated with the emergence of new GII.4 variants. Taken together, our data map antibody and HBGA carbohydrate binding to proximal regions of the norovirus capsid, showing that evolutionary pressures on the norovirus capsid protein may affect both antigenic and carbohydrate recognition phenotypes. PMID:22532688

Concept Mapping as a Tool to Develop and Measure Students' Understanding in Science

ERIC Educational Resources Information Center

Tan, Sema; Erdimez, Omer; Zimmerman, Robert

2017-01-01

Concept maps measured a student's understanding of the complexity of concepts, and interrelationships. Novak and Gowin (1984) claimed that the continuous use of concept maps increased the complexity and interconnectedness of students' understanding of relationships between concepts in a particular science domain. This study has two purposes; the…

Concept Mapping Assessment of Media Assisted Learning in Interdisciplinary Science Education

NASA Astrophysics Data System (ADS)

Schaal, Steffen; Bogner, Franz X.; Girwidz, Raimund

2010-05-01

Acquisition of conceptual knowledge is a central aim in science education. In this study we monitored an interdisciplinary hypermedia assisted learning unit on hibernation and thermodynamics based on cooperative learning. We used concept mapping for the assessment, applying a pre-test/post-test design. In our study, 106 9th graders cooperated by working in pairs ( n = 53) for six lessons. As an interdisciplinary learning activity in such complex knowledge domains has to combine many different aspects, we focused on long-term knowledge. Learners working cooperatively in dyads constructed computer-supported concept maps which were analysed by specific software. The data analysis encompassed structural aspects of the knowledge corresponding to a target reference map. After the learning unit, the results showed the acquisition of higher-order domain-specific knowledge structures which indicates successful interdisciplinary learning through the hypermedia learning environment. The benefit of using a computer-assisted concept mapping assessment for research in science education, and in science classrooms is considered.

Multiclass Continuous Correspondence Learning

NASA Technical Reports Server (NTRS)

Bue, Brian D,; Thompson, David R.

2011-01-01

We extend the Structural Correspondence Learning (SCL) domain adaptation algorithm of Blitzer er al. to the realm of continuous signals. Given a set of labeled examples belonging to a 'source' domain, we select a set of unlabeled examples in a related 'target' domain that play similar roles in both domains. Using these 'pivot samples, we map both domains into a common feature space, allowing us to adapt a classifier trained on source examples to classify target examples. We show that when between-class distances are relatively preserved across domains, we can automatically select target pivots to bring the domains into correspondence.

Semantics driven approach for knowledge acquisition from EMRs.

PubMed

Perera, Sujan; Henson, Cory; Thirunarayan, Krishnaprasad; Sheth, Amit; Nair, Suhas

2014-03-01

Semantic computing technologies have matured to be applicable to many critical domains such as national security, life sciences, and health care. However, the key to their success is the availability of a rich domain knowledge base. The creation and refinement of domain knowledge bases pose difficult challenges. The existing knowledge bases in the health care domain are rich in taxonomic relationships, but they lack nontaxonomic (domain) relationships. In this paper, we describe a semiautomatic technique for enriching existing domain knowledge bases with causal relationships gleaned from Electronic Medical Records (EMR) data. We determine missing causal relationships between domain concepts by validating domain knowledge against EMR data sources and leveraging semantic-based techniques to derive plausible relationships that can rectify knowledge gaps. Our evaluation demonstrates that semantic techniques can be employed to improve the efficiency of knowledge acquisition.

Osmostress induces autophosphorylation of Hog1 via a C-terminal regulatory region that is conserved in p38α.

PubMed

Maayan, Inbal; Beenstock, Jonah; Marbach, Irit; Tabachnick, Shira; Livnah, Oded; Engelberg, David

2012-01-01

Many protein kinases require phosphorylation at their activation loop for induction of catalysis. Mitogen-activated protein kinases (MAPKs) are activated by a unique mode of phosphorylation, on neighboring Tyrosine and Threonine residues. Whereas many kinases obtain their activation via autophosphorylation, MAPKs are usually phosphorylated by specific, dedicated, MAPK kinases (MAP2Ks). Here we show however, that the yeast MAPK Hog1, known to be activated by the MAP2K Pbs2, is activated in pbs2Δ cells via an autophosphorylation activity that is induced by osmotic pressure. We mapped a novel domain at the Hog1 C-terminal region that inhibits this activity. Removal of this domain provides a Hog1 protein that is partially independent of MAP2K, namely, partially rescues osmostress sensitivity of pbs2Δ cells. We further mapped a short domain (7 amino acid residues long) that is critical for induction of autophosphorylation. Its removal abolishes autophosphorylation, but maintains Pbs2-mediated phosphorylation. This 7 amino acids stretch is conserved in the human p38α. Similar to the case of Hog1, it's removal from p38α abolishes p38α's autophosphorylation capability, but maintains, although reduces, its activation by MKK6. This study joins a few recent reports to suggest that, like many protein kinases, MAPKs are also regulated via induced autoactivation.

Osmostress Induces Autophosphorylation of Hog1 via a C-Terminal Regulatory Region That Is Conserved in p38α

PubMed Central

Maayan, Inbal; Beenstock, Jonah; Marbach, Irit; Tabachnick, Shira; Livnah, Oded; Engelberg, David

2012-01-01

Many protein kinases require phosphorylation at their activation loop for induction of catalysis. Mitogen-activated protein kinases (MAPKs) are activated by a unique mode of phosphorylation, on neighboring Tyrosine and Threonine residues. Whereas many kinases obtain their activation via autophosphorylation, MAPKs are usually phosphorylated by specific, dedicated, MAPK kinases (MAP2Ks). Here we show however, that the yeast MAPK Hog1, known to be activated by the MAP2K Pbs2, is activated in pbs2Δ cells via an autophosphorylation activity that is induced by osmotic pressure. We mapped a novel domain at the Hog1 C-terminal region that inhibits this activity. Removal of this domain provides a Hog1 protein that is partially independent of MAP2K, namely, partially rescues osmostress sensitivity of pbs2Δ cells. We further mapped a short domain (7 amino acid residues long) that is critical for induction of autophosphorylation. Its removal abolishes autophosphorylation, but maintains Pbs2-mediated phosphorylation. This 7 amino acids stretch is conserved in the human p38α. Similar to the case of Hog1, it’s removal from p38α abolishes p38α’s autophosphorylation capability, but maintains, although reduces, its activation by MKK6. This study joins a few recent reports to suggest that, like many protein kinases, MAPKs are also regulated via induced autoactivation. PMID:22984552

The Data Transfer Kit: A geometric rendezvous-based tool for multiphysics data transfer

DOE Office of Scientific and Technical Information (OSTI.GOV)

Slattery, S. R.; Wilson, P. P. H.; Pawlowski, R. P.

2013-07-01

The Data Transfer Kit (DTK) is a software library designed to provide parallel data transfer services for arbitrary physics components based on the concept of geometric rendezvous. The rendezvous algorithm provides a means to geometrically correlate two geometric domains that may be arbitrarily decomposed in a parallel simulation. By repartitioning both domains such that they have the same geometric domain on each parallel process, efficient and load balanced search operations and data transfer can be performed at a desirable algorithmic time complexity with low communication overhead relative to other types of mapping algorithms. With the increased development efforts in multiphysicsmore » simulation and other multiple mesh and geometry problems, generating parallel topology maps for transferring fields and other data between geometric domains is a common operation. The algorithms used to generate parallel topology maps based on the concept of geometric rendezvous as implemented in DTK are described with an example using a conjugate heat transfer calculation and thermal coupling with a neutronics code. In addition, we provide the results of initial scaling studies performed on the Jaguar Cray XK6 system at Oak Ridge National Laboratory for a worse-case-scenario problem in terms of algorithmic complexity that shows good scaling on 0(1 x 104) cores for topology map generation and excellent scaling on 0(1 x 105) cores for the data transfer operation with meshes of O(1 x 109) elements. (authors)« less

Initial constructs for patient-centered outcome measures to evaluate brain-computer interfaces.

PubMed

Andresen, Elena M; Fried-Oken, Melanie; Peters, Betts; Patrick, Donald L

2016-10-01

The authors describe preliminary work toward the creation of patient-centered outcome (PCO) measures to evaluate brain-computer interface (BCI) as an assistive technology (AT) for individuals with severe speech and physical impairments (SSPI). In Phase 1, 591 items from 15 existing measures were mapped to the International Classification of Functioning, Disability and Health (ICF). In Phase 2, qualitative interviews were conducted with eight people with SSPI and seven caregivers. Resulting text data were coded in an iterative analysis. Most items (79%) were mapped to the ICF environmental domain; over half (53%) were mapped to more than one domain. The ICF framework was well suited for mapping items related to body functions and structures, but less so for items in other areas, including personal factors. Two constructs emerged from qualitative data: quality of life (QOL) and AT. Component domains and themes were identified for each. Preliminary constructs, domains and themes were generated for future PCO measures relevant to BCI. Existing instruments are sufficient for initial items but do not adequately match the values of people with SSPI and their caregivers. Field methods for interviewing people with SSPI were successful, and support the inclusion of these individuals in PCO research. Implications for Rehabilitation Adapted interview methods allow people with severe speech and physical impairments to participate in patient-centered outcomes research. Patient-centered outcome measures are needed to evaluate the clinical implementation of brain-computer interface as an assistive technology.

Pulmonary rehabilitation referral and participation are commonly influenced by environment, knowledge, and beliefs about consequences: a systematic review using the Theoretical Domains Framework.

PubMed

Cox, Narelle S; Oliveira, Cristino C; Lahham, Aroub; Holland, Anne E

2017-04-01

What are the barriers and enablers of referral, uptake, attendance and completion of pulmonary rehabilitation for people with chronic obstructive pulmonary disease (COPD)? Systematic review of qualitative or quantitative studies reporting data relating to referral, uptake, attendance and/or completion in pulmonary rehabilitation. People aged >18years with a diagnosis of COPD and/or their healthcare professionals. Data were extracted regarding the nature of barriers and enablers of pulmonary rehabilitation referral and participation. Extracted data items were mapped to the Theoretical Domains Framework (TDF). A total of 6969 references were screened, with 48 studies included and 369 relevant items mapped to the TDF. The most frequently represented domain was 'Environment' (33/48 included studies, 37% of mapped items), which included items such as waiting time, burden of illness, travel, transport and health system resources. Other frequently represented domains were 'Knowledge' (18/48 studies, including items such as clinician knowledge of referral processes, patient understanding of rehabilitation content) and 'Beliefs about consequences' (15/48 studies, including items such as beliefs regarding role and safety of exercise, expectations of rehabilitation outcomes). Barriers to referral, uptake, attendance or completion represented 71% (n=183) of items mapped to the TDF. All domains of the TDF were represented; however, items were least frequently coded to the domains of 'Optimism' and 'Memory'. The methodological quality of included studies was fair (mean quality score 9/12, SD 2). Many factors - particularly those related to environment, knowledge, attitudes and behaviours - interact to influence referral, uptake, attendance and completion of pulmonary rehabilitation. Overcoming the challenges associated with the personal and/or healthcare system environment will be imperative to improving access and uptake of pulmonary rehabilitation. PROSPERO CRD42015015976. [Cox NS, Oliveira CC, Lahham A, Holland AE (2017) Pulmonary rehabilitation referral and participation are commonly influenced by environment, knowledge, and beliefs about consequences: a systematic review using the Theoretical Domains Framework. Journal of Physiotherapy 63: 84-93]. Copyright © 2017 Australian Physiotherapy Association. Published by Elsevier B.V. All rights reserved.

Large-Scale, High-Resolution Neurophysiological Maps Underlying fMRI of Macaque Temporal Lobe

PubMed Central

Papanastassiou, Alex M.; DiCarlo, James J.

2013-01-01

Maps obtained by functional magnetic resonance imaging (fMRI) are thought to reflect the underlying spatial layout of neural activity. However, previous studies have not been able to directly compare fMRI maps to high-resolution neurophysiological maps, particularly in higher level visual areas. Here, we used a novel stereo microfocal x-ray system to localize thousands of neural recordings across monkey inferior temporal cortex (IT), construct large-scale maps of neuronal object selectivity at subvoxel resolution, and compare those neurophysiology maps with fMRI maps from the same subjects. While neurophysiology maps contained reliable structure at the sub-millimeter scale, fMRI maps of object selectivity contained information at larger scales (>2.5 mm) and were only partly correlated with raw neurophysiology maps collected in the same subjects. However, spatial smoothing of neurophysiology maps more than doubled that correlation, while a variety of alternative transforms led to no significant improvement. Furthermore, raw spiking signals, once spatially smoothed, were as predictive of fMRI maps as local field potential signals. Thus, fMRI of the inferior temporal lobe reflects a spatially low-passed version of neurophysiology signals. These findings strongly validate the widespread use of fMRI for detecting large (>2.5 mm) neuronal domains of object selectivity but show that a complete understanding of even the most pure domains (e.g., faces vs nonface objects) requires investigation at fine scales that can currently only be obtained with invasive neurophysiological methods. PMID:24048850

Combining Techniques to Refine Item to Skills Q-Matrices with a Partition Tree

ERIC Educational Resources Information Center

Desmarais, Michel C.; Xu, Peng; Beheshti, Behzad

2015-01-01

The problem of mapping items to skills is gaining interest with the emergence of recent techniques that can use data for both defining this mapping, and for refining mappings given by experts. We investigate the problem of refining mapping from an expert by combining the output of different techniques. The combination is based on a partition tree…

The role of the hippocampus in navigation is memory

PubMed Central

2017-01-01

There is considerable research on the neurobiological mechanisms within the hippocampal system that support spatial navigation. In this article I review the literature on navigational strategies in humans and animals, observations on hippocampal function in navigation, and studies of hippocampal neural activity in animals and humans performing different navigational tasks and tests of memory. Whereas the hippocampus is essential to spatial navigation via a cognitive map, its role derives from the relational organization and flexibility of cognitive maps and not from a selective role in the spatial domain. Correspondingly, hippocampal networks map multiple navigational strategies, as well as other spatial and nonspatial memories and knowledge domains that share an emphasis on relational organization. These observations suggest that the hippocampal system is not dedicated to spatial cognition and navigation, but organizes experiences in memory, for which spatial mapping and navigation are both a metaphor for and a prominent application of relational memory organization. PMID:28148640

Surface Design Based on Discrete Conformal Transformations

NASA Astrophysics Data System (ADS)

Duque, Carlos; Santangelo, Christian; Vouga, Etienne

Conformal transformations are angle-preserving maps from one domain to another. Although angles are preserved, the lengths between arbitrary points are not generally conserved. As a consequence there is always a given amount of distortion associated to any conformal map. Different uses of such transformations can be found in various fields, but have been used by us to program non-uniformly swellable gel sheets to buckle into prescribed three dimensional shapes. In this work we apply circle packings as a kind of discrete conformal map in order to find conformal maps from the sphere to the plane that can be used as nearly uniform swelling patterns to program non-Euclidean sheets to buckle into spheres. We explore the possibility of tuning the area distortion to fit the experimental range of minimum and maximum swelling by modifying the boundary of the planar domain through the introduction of different cutting schemes.

Natural speech reveals the semantic maps that tile human cerebral cortex

PubMed Central

Huth, Alexander G.; de Heer, Wendy A.; Griffiths, Thomas L.; Theunissen, Frédéric E.; Gallant, Jack L.

2016-01-01

The meaning of language is represented in regions of the cerebral cortex collectively known as the “semantic system”. However, little of the semantic system has been mapped comprehensively, and the semantic selectivity of most regions is unknown. Here we systematically map semantic selectivity across the cortex using voxel-wise modeling of fMRI data collected while subjects listened to hours of narrative stories. We show that the semantic system is organized into intricate patterns that appear consistent across individuals. We then use a novel generative model to create a detailed semantic atlas. Our results suggest that most areas within the semantic system represent information about specific semantic domains, or groups of related concepts, and our atlas shows which domains are represented in each area. This study demonstrates that data-driven methods—commonplace in studies of human neuroanatomy and functional connectivity—provide a powerful and efficient means for mapping functional representations in the brain. PMID:27121839

Capturing the Integration of Practice-Based Learning with Beliefs, Values, and Attitudes using Modified Concept Mapping.

PubMed

Mcnaughton, Susan; Barrow, Mark; Bagg, Warwick; Frielick, Stanley

2016-01-01

Practice-based learning integrates the cognitive, psychomotor, and affective domains and is influenced by students' beliefs, values, and attitudes. Concept mapping has been shown to effectively demonstrate students' changing concepts and knowledge structures. This article discusses how concept mapping was modified to capture students' perceptions of the connections between the domains of thinking and knowing, emotions, behavior, attitudes, values, and beliefs and the specific experiences related to these, over a period of eight months of practice-based clinical learning. The findings demonstrate that while some limitations exist, modified concept mapping is a manageable way to gather rich data about students' perceptions of their clinical practice experiences. These findings also highlight the strong integrating influence of beliefs and values on other areas of practice, suggesting that these need to be attended to as part of a student's educational program.

Capturing the Integration of Practice-Based Learning with Beliefs, Values, and Attitudes using Modified Concept Mapping

PubMed Central

Mcnaughton, Susan; Barrow, Mark; Bagg, Warwick; Frielick, Stanley

2016-01-01

Practice-based learning integrates the cognitive, psychomotor, and affective domains and is influenced by students’ beliefs, values, and attitudes. Concept mapping has been shown to effectively demonstrate students’ changing concepts and knowledge structures. This article discusses how concept mapping was modified to capture students’ perceptions of the connections between the domains of thinking and knowing, emotions, behavior, attitudes, values, and beliefs and the specific experiences related to these, over a period of eight months of practice-based clinical learning. The findings demonstrate that while some limitations exist, modified concept mapping is a manageable way to gather rich data about students’ perceptions of their clinical practice experiences. These findings also highlight the strong integrating influence of beliefs and values on other areas of practice, suggesting that these need to be attended to as part of a student's educational program. PMID:29349311

Identification and analysis of mutational hotspots in oncogenes and tumour suppressors.

PubMed

Baeissa, Hanadi; Benstead-Hume, Graeme; Richardson, Christopher J; Pearl, Frances M G

2017-03-28

The key to interpreting the contribution of a disease-associated mutation in the development and progression of cancer is an understanding of the consequences of that mutation both on the function of the affected protein and on the pathways in which that protein is involved. Protein domains encapsulate function and position-specific domain based analysis of mutations have been shown to help elucidate their phenotypes. In this paper we examine the domain biases in oncogenes and tumour suppressors, and find that their domain compositions substantially differ. Using data from over 30 different cancers from whole-exome sequencing cancer genomic projects we mapped over one million mutations to their respective Pfam domains to identify which domains are enriched in any of three different classes of mutation; missense, indels or truncations. Next, we identified the mutational hotspots within domain families by mapping small mutations to equivalent positions in multiple sequence alignments of protein domainsWe find that gain of function mutations from oncogenes and loss of function mutations from tumour suppressors are normally found in different domain families and when observed in the same domain families, hotspot mutations are located at different positions within the multiple sequence alignment of the domain. By considering hotspots in tumour suppressors and oncogenes independently, we find that there are different specific positions within domain families that are particularly suited to accommodate either a loss or a gain of function mutation. The position is also dependent on the class of mutation.We find rare mutations co-located with well-known functional mutation hotspots, in members of homologous domain superfamilies, and we detect novel mutation hotspots in domain families previously unconnected with cancer. The results of this analysis can be accessed through the MOKCa database (http://strubiol.icr.ac.uk/extra/MOKCa).

Development of a New Time-Resolved Laser-Induced Fluorescence Technique

NASA Astrophysics Data System (ADS)

Durot, Christopher; Gallimore, Alec

2012-10-01

We are developing a time-resolved laser-induced fluorescence (LIF) technique to interrogate the ion velocity distribution function (VDF) of EP thruster plumes down to the microsecond time scale. Better measurements of dynamic plasma processes will lead to improvements in simulation and prediction of thruster operation and erosion. We present the development of the new technique and results of initial tests. Signal-to-noise ratio (SNR) is often a challenge for LIF studies, and it is only more challenging for time-resolved measurements since a lock-in amplifier cannot be used with a long time constant. The new system uses laser modulation on the order of MHz, which enables the use of electronic filtering and phase-sensitive detection to improve SNR while preserving time-resolved information. Statistical averaging over many cycles to further improve SNR is done in the frequency domain. This technique can have significant advantages, including (1) larger spatial maps enabled by shorter data acquisition time and (2) the ability to average data without creating a phase reference by modifying the thruster operating condition with a periodic cutoff in discharge current, which can modify the ion velocity distribution.

Imaging brain microstructure with diffusion MRI: practicality and applications.

PubMed

Alexander, Daniel C; Dyrby, Tim B; Nilsson, Markus; Zhang, Hui

2017-11-29

This article gives an overview of microstructure imaging of the brain with diffusion MRI and reviews the state of the art. The microstructure-imaging paradigm aims to estimate and map microscopic properties of tissue using a model that links these properties to the voxel scale MR signal. Imaging techniques of this type are just starting to make the transition from the technical research domain to wide application in biomedical studies. We focus here on the practicalities of both implementing such techniques and using them in applications. Specifically, the article summarizes the relevant aspects of brain microanatomy and the range of diffusion-weighted MR measurements that provide sensitivity to them. It then reviews the evolution of mathematical and computational models that relate the diffusion MR signal to brain tissue microstructure, as well as the expanding areas of application. Next we focus on practicalities of designing a working microstructure imaging technique: model selection, experiment design, parameter estimation, validation, and the pipeline of development of this class of technique. The article concludes with some future perspectives on opportunities in this topic and expectations on how the field will evolve in the short-to-medium term. Copyright © 2017 John Wiley & Sons, Ltd.

Domain mapping of the Rad51 paralog protein complexes

PubMed Central

Miller, Kristi A.; Sawicka, Dorota; Barsky, Daniel; Albala, Joanna S.

2004-01-01

The five human Rad51 paralogs are suggested to play an important role in the maintenance of genome stability through their function in DNA double-strand break repair. These proteins have been found to form two distinct complexes in vivo, Rad51B–Rad51C–Rad51D–Xrcc2 (BCDX2) and Rad51C–Xrcc3 (CX3). Based on the recent Pyrococcus furiosus Rad51 structure, we have used homology modeling to design deletion mutants of the Rad51 paralogs. The models of the human Rad51B, Rad51C, Xrcc3 and murine Rad51D (mRad51D) proteins reveal distinct N-terminal and C-terminal domains connected by a linker region. Using yeast two-hybrid and co-immunoprecipitation techniques, we have demonstrated that a fragment of Rad51B containing amino acid residues 1–75 interacts with the C-terminus and linker of Rad51C, residues 79–376, and this region of Rad51C also interacts with mRad51D and Xrcc3. We have also determined that the N-terminal domain of mRad51D, residues 4–77, binds to Xrcc2 while the C-terminal domain of mRad51D, residues 77–328, binds Rad51C. By this, we have identified the binding domains of the BCDX2 and CX3 complexes to further characterize the interaction of these proteins and propose a scheme for the three-dimensional architecture of the BCDX2 and CX3 paralog complexes. PMID:14704354

Split-probe hybrid femtosecond/picosecond rotational CARS for time-domain measurement of S-branch Raman linewidths within a single laser shot.

PubMed

Patterson, Brian D; Gao, Yi; Seeger, Thomas; Kliewer, Christopher J

2013-11-15

We introduce a multiplex technique for the single-laser-shot determination of S-branch Raman linewidths with high accuracy and precision by implementing hybrid femtosecond (fs)/picosecond (ps) rotational coherent anti-Stokes Raman spectroscopy (CARS) with multiple spatially and temporally separated probe beams derived from a single laser pulse. The probe beams scatter from the rotational coherence driven by the fs pump and Stokes pulses at four different probe pulse delay times spanning 360 ps, thereby mapping collisional coherence dephasing in time for the populated rotational levels. The probe beams scatter at different folded BOXCARS angles, yielding spatially separated CARS signals which are collected simultaneously on the charge coupled device camera. The technique yields a single-shot standard deviation (1σ) of less than 3.5% in the determination of Raman linewidths and the average linewidth values obtained for N(2) are within 1% of those previously reported. The presented technique opens the possibility for correcting CARS spectra for time-varying collisional environments in operando.

The Effects of a Concept Map-Based Support Tool on Simulation-Based Inquiry Learning

ERIC Educational Resources Information Center

Hagemans, Mieke G.; van der Meij, Hans; de Jong, Ton

2013-01-01

Students often need support to optimize their learning in inquiry learning environments. In 2 studies, we investigated the effects of adding concept-map-based support to a simulation-based inquiry environment on kinematics. The concept map displayed the main domain concepts and their relations, while dynamic color coding of the concepts displayed…

Visualizing the Logistic Map with a Microcontroller

ERIC Educational Resources Information Center

Serna, Juan D.; Joshi, Amitabh

2012-01-01

The logistic map is one of the simplest nonlinear dynamical systems that clearly exhibits the route to chaos. In this paper, we explore the evolution of the logistic map using an open-source microcontroller connected to an array of light-emitting diodes (LEDs). We divide the one-dimensional domain interval [0,1] into ten equal parts, an associate…

A New Southern North Atlantic Isochron Map: Insights Into the Drift of the Iberian Plate Since the Late Cretaceous

NASA Astrophysics Data System (ADS)

Macchiavelli, Chiara; Vergés, Jaume; Schettino, Antonio; Fernández, Manel; Turco, Eugenio; Casciello, Emilio; Torne, Montserrat; Pierantoni, Pietro Paolo; Tunini, Lavinia

2017-12-01

This paper presents a new southern North Atlantic plate model from Late Cretaceous to present, with the aim of constraining the kinematics of the Iberian plate during the last 83.5 Myr. This model is presented along with a detailed isochron map generated through the analysis of 3 aeromagnetic tracks and 400 ship tracks from the National Centers for Environmental Information database. We present a new technique to obtain well-constrained estimates of the Iberia-North America plate motions from magnetic anomalies, overcoming the scarcity of large-offset fracture zones and transform faults. We build an integrated kinematic model for NW Africa, Morocco, Iberia, Europe, and North America, which shows that the deformation is partitioned between Pyrenees and Betic-Rif orogenic domain during the Late Cretaceous-Oligocene time interval. In the Eastern Betics domain, the calculated amount of NW Africa-Iberia convergence is 80 km between 83.5 and 34 Ma, followed by 150 km since the Oligocene. The motion of Iberia relative to Europe in the Central Pyrenees is characterized by overall NE directed transpressional motion during the Campanian and the Paleocene, followed by NW directed transpressional movement until the Lutetian and overall NNW directed convergence from Bartonian to Chattian. This motion occurs along the axis of the Bay of Biscay from the Santonian-Campanian boundary to the middle Priabonian, subsequently jumping to King's Trough at Anomaly 17 (36.62 Ma).

Brain Surface Conformal Parameterization Using Riemann Surface Structure

PubMed Central

Wang, Yalin; Lui, Lok Ming; Gu, Xianfeng; Hayashi, Kiralee M.; Chan, Tony F.; Toga, Arthur W.; Thompson, Paul M.; Yau, Shing-Tung

2011-01-01

In medical imaging, parameterized 3-D surface models are useful for anatomical modeling and visualization, statistical comparisons of anatomy, and surface-based registration and signal processing. Here we introduce a parameterization method based on Riemann surface structure, which uses a special curvilinear net structure (conformal net) to partition the surface into a set of patches that can each be conformally mapped to a parallelogram. The resulting surface subdivision and the parameterizations of the components are intrinsic and stable (their solutions tend to be smooth functions and the boundary conditions of the Dirichlet problem can be enforced). Conformal parameterization also helps transform partial differential equations (PDEs) that may be defined on 3-D brain surface manifolds to modified PDEs on a two-dimensional parameter domain. Since the Jacobian matrix of a conformal parameterization is diagonal, the modified PDE on the parameter domain is readily solved. To illustrate our techniques, we computed parameterizations for several types of anatomical surfaces in 3-D magnetic resonance imaging scans of the brain, including the cerebral cortex, hippocampi, and lateral ventricles. For surfaces that are topologically homeomorphic to each other and have similar geometrical structures, we show that the parameterization results are consistent and the subdivided surfaces can be matched to each other. Finally, we present an automatic sulcal landmark location algorithm by solving PDEs on cortical surfaces. The landmark detection results are used as constraints for building conformal maps between surfaces that also match explicitly defined landmarks. PMID:17679336

In vivo correlation mapping microscopy

NASA Astrophysics Data System (ADS)

McGrath, James; Alexandrov, Sergey; Owens, Peter; Subhash, Hrebesh; Leahy, Martin

2016-04-01

To facilitate regular assessment of the microcirculation in vivo, noninvasive imaging techniques such as nailfold capillaroscopy are required in clinics. Recently, a correlation mapping technique has been applied to optical coherence tomography (OCT), which extends the capabilities of OCT to microcirculation morphology imaging. This technique, known as correlation mapping optical coherence tomography, has been shown to extract parameters, such as capillary density and vessel diameter, and key clinical markers associated with early changes in microvascular diseases. However, OCT has limited spatial resolution in both the transverse and depth directions. Here, we extend this correlation mapping technique to other microscopy modalities, including confocal microscopy, and take advantage of the higher spatial resolution offered by these modalities. The technique is achieved as a processing step on microscopy images and does not require any modification to the microscope hardware. Results are presented which show that this correlation mapping microscopy technique can extend the capabilities of conventional microscopy to enable mapping of vascular networks in vivo with high spatial resolution in both the transverse and depth directions.

A new watermarking approach based on combination of reversible watermarking and CDMA in spatial and DWT domain

NASA Astrophysics Data System (ADS)

Bekkouche, S.; Chouarfia, A.

2011-06-01

Image watermarking can be defined as a technique that allows insertion of imperceptible and indelible digital data into an image. In addition to its initial application which is the copyright, watermarking can be used in other fields, particularly in the medical field in order to contribute to secure images shared on the network for telemedicine applications. In this report we study some watermarking methods and the comparison result of their combination, the first one is based on the CDMA (Code Division Multiple Access) in DWT and spatial domain and its aim is to verify the image authenticity whereas the second one is the reversible watermarking (the least significant bits LSB and cryptography tools) and the reversible contrast mapping RCM its objective is to check the integrity of the image and to keep the Confidentiality of the patient data. A new scheme of watermarking is the combination of the reversible watermarking method based on LSB and cryptography tools and the method of CDMA in spatial and DWT domain to verify the three security properties Integrity, Authenticity and confidentiality of medical data and patient information .In the end ,we made a comparison between these methods within the parameters of quality of medical images. Initially, an in-depth study on the characteristics of medical images would contribute to improve these methods to mitigate their limits and to optimize the results. Tests were done on IRM kind of medical images and the quality measurements have been done on the watermarked image to verify that this technique does not lead to a wrong diagnostic. The robustness of the watermarked images against attacks has been verified on the parameters of PSNR, SNR, MSE and MAE which the experimental result demonstrated that the proposed algorithm is good and robust in DWT than in spatial domain.

A Tangible Approach to Concept Mapping

NASA Astrophysics Data System (ADS)

Tanenbaum, Karen; Antle, Alissa N.

2009-05-01

The Tangible Concept Mapping project investigates using a tangible user interface to engage learners in concept map creation. This paper describes a prototype implementation of the system, presents some preliminary analysis of its ease of use and effectiveness, and discusses how elements of tangible interaction support concept mapping by helping users organize and structure their knowledge about a domain. The role of physical engagement and embodiment in supporting the mental activity of creating the concept map is explored as one of the benefits of a tangible approach to learning.

Digital Mapping Techniques '09-Workshop Proceedings, Morgantown, West Virginia, May 10-13, 2009

USGS Publications Warehouse

Soller, David R.

2011-01-01

As in the previous years' meetings, the objective was to foster informal discussion and exchange of technical information, principally in order to develop more efficient methods for digital mapping, cartography, GIS analysis, and information management. At this meeting, oral and poster presentations and special discussion sessions emphasized (1) methods for creating and publishing map products (here, "publishing" includes Web-based release); (2) field data capture software and techniques, including the use of LiDAR; (3) digital cartographic techniques; (4) migration of digital maps into ArcGIS Geodatabase format; (5) analytical GIS techniques; and (6) continued development of the National Geologic Map Database.

The role of MAP4K3 in lifespan regulation of Caenorhabditiselegans

DOE Office of Scientific and Technical Information (OSTI.GOV)

Khan, Maruf H.; Hart, Matthew J., E-mail: HartMJ@uthscsa.edu; Rea, Shane L., E-mail: reas3@uthscsa.edu

2012-08-24

Highlights: Black-Right-Pointing-Pointer Inhibition of MAP4K3 by RNAi leads to increased mean lifespan in Caenorhabditis elegans. Black-Right-Pointing-Pointer Mutation in the citron homology domain of MAP4K3 leads to increased mean lifespan. Black-Right-Pointing-Pointer Mutation in the kinase domain of MAP4K3 has no significant effect on mean lifespan. -- Abstract: The TOR pathway is a kinase signaling pathway that regulates cellular growth and proliferation in response to nutrients and growth factors. TOR signaling is also important in lifespan regulation - when this pathway is inhibited, either naturally, by genetic mutation, or by pharmacological means, lifespan is extended. MAP4K3 is a Ser/Thr kinase that hasmore » recently been found to be involved in TOR activation. Unexpectedly, the effect of this protein is not mediated via Rheb, the more widely known TOR activation pathway. Given the role of TOR in growth and lifespan control, we looked at how inhibiting MAP4K3 in Caenorhabditiselegans affects lifespan. We used both feeding RNAi and genetic mutants to look at the effect of MAP4K3 deficiency. Our results show a small but significant increase in mean lifespan in MAP4K3 deficient worms. MAP4K3 thus represents a new target in the TOR pathway that can be targeted for pharmacological intervention to control lifespan.« less

Resident Space Object Characterization and Behavior Understanding via Machine Learning and Ontology-based Bayesian Networks

NASA Astrophysics Data System (ADS)

Furfaro, R.; Linares, R.; Gaylor, D.; Jah, M.; Walls, R.

2016-09-01

In this paper, we present an end-to-end approach that employs machine learning techniques and Ontology-based Bayesian Networks (BN) to characterize the behavior of resident space objects. State-of-the-Art machine learning architectures (e.g. Extreme Learning Machines, Convolutional Deep Networks) are trained on physical models to learn the Resident Space Object (RSO) features in the vectorized energy and momentum states and parameters. The mapping from measurements to vectorized energy and momentum states and parameters enables behavior characterization via clustering in the features space and subsequent RSO classification. Additionally, Space Object Behavioral Ontologies (SOBO) are employed to define and capture the domain knowledge-base (KB) and BNs are constructed from the SOBO in a semi-automatic fashion to execute probabilistic reasoning over conclusions drawn from trained classifiers and/or directly from processed data. Such an approach enables integrating machine learning classifiers and probabilistic reasoning to support higher-level decision making for space domain awareness applications. The innovation here is to use these methods (which have enjoyed great success in other domains) in synergy so that it enables a "from data to discovery" paradigm by facilitating the linkage and fusion of large and disparate sources of information via a Big Data Science and Analytics framework.

Spatially constrained Bayesian inversion of frequency- and time-domain electromagnetic data from the Tellus projects

NASA Astrophysics Data System (ADS)

Kiyan, Duygu; Rath, Volker; Delhaye, Robert

2017-04-01

The frequency- and time-domain airborne electromagnetic (AEM) data collected under the Tellus projects of the Geological Survey of Ireland (GSI) which represent a wealth of information on the multi-dimensional electrical structure of Ireland's near-surface. Our project, which was funded by GSI under the framework of their Short Call Research Programme, aims to develop and implement inverse techniques based on various Bayesian methods for these densely sampled data. We have developed a highly flexible toolbox using Python language for the one-dimensional inversion of AEM data along the flight lines. The computational core is based on an adapted frequency- and time-domain forward modelling core derived from the well-tested open-source code AirBeo, which was developed by the CSIRO (Australia) and the AMIRA consortium. Three different inversion methods have been implemented: (i) Tikhonov-type inversion including optimal regularisation methods (Aster el al., 2012; Zhdanov, 2015), (ii) Bayesian MAP inversion in parameter and data space (e.g. Tarantola, 2005), and (iii) Full Bayesian inversion with Markov Chain Monte Carlo (Sambridge and Mosegaard, 2002; Mosegaard and Sambridge, 2002), all including different forms of spatial constraints. The methods have been tested on synthetic and field data. This contribution will introduce the toolbox and present case studies on the AEM data from the Tellus projects.

Separation of Migration and Tomography Modes of Full-Waveform Inversion in the Plane Wave Domain

NASA Astrophysics Data System (ADS)

Yao, Gang; da Silva, Nuno V.; Warner, Michael; Kalinicheva, Tatiana

2018-02-01

Full-waveform inversion (FWI) includes both migration and tomography modes. The migration mode acts like a nonlinear least squares migration to map model interfaces with reflections, while the tomography mode behaves as tomography to build a background velocity model. The migration mode is the main response of inverting reflections, while the tomography mode exists in response to inverting both the reflections and refractions. To emphasize one of the two modes in FWI, especially for inverting reflections, the separation of the two modes in the gradient of FWI is required. Here we present a new method to achieve this separation with an angle-dependent filtering technique in the plane wave domain. We first transform the source and residual wavefields into the plane wave domain with the Fourier transform and then decompose them into the migration and tomography components using the opening angles between the transformed source and residual plane waves. The opening angles close to 180° contribute to the tomography component, while the others correspond to the migration component. We find that this approach is very effective and robust even when the medium is relatively complicated with strong lateral heterogeneities, highly dipping reflectors, and strong anisotropy. This is well demonstrated by theoretical analysis and numerical tests with a synthetic data set and a field data set.

Brain connectivity study of joint attention using frequency-domain optical imaging technique

NASA Astrophysics Data System (ADS)

Chaudhary, Ujwal; Zhu, Banghe; Godavarty, Anuradha

2010-02-01

Autism is a socio-communication brain development disorder. It is marked by degeneration in the ability to respond to joint attention skill task, from as early as 12 to 18 months of age. This trait is used to distinguish autistic from nonautistic populations. In this study, diffuse optical imaging is being used to study brain connectivity for the first time in response to joint attention experience in normal adults. The prefrontal region of the brain was non-invasively imaged using a frequency-domain based optical imager. The imaging studies were performed on 11 normal right-handed adults and optical measurements were acquired in response to joint-attention based video clips. While the intensity-based optical data provides information about the hemodynamic response of the underlying neural process, the time-dependent phase-based optical data has the potential to explicate the directional information on the activation of the brain. Thus brain connectivity studies are performed by computing covariance/correlations between spatial units using this frequency-domain based optical measurements. The preliminary results indicate that the extent of synchrony and directional variation in the pattern of activation varies in the left and right frontal cortex. The results have significant implication for research in neural pathways associated with autism that can be mapped using diffuse optical imaging tools in the future.

Analysis of Investment IT Planning on Logistic Company Using COBIT 5

NASA Astrophysics Data System (ADS)

Fachri Pane, Syafrial; Maulana Awangga, Rolly; Nuraini, Rd.; Fathonah, Siti

2018-04-01

IT Investment planning to review goals business strategy development needs to support IT governance. Planning its investments will be assessed with a framework is issued by ISACA that COBIT 5 focus on domain EDM, APO, BAI, and MEA. Mapping from framework COBIT 5 with Val IT lead nine domain consisting of EDM01, EDM02, APO01, APO02, APO05, APO06, APO07, BAI01, and MEA01. Article search google using RACI diagram generating mapping organisation telecoms and authority structures for the review identify respondents from any domain. Under selected area be used to review counting process capability level, and for a discussion of development, priorities make recommendations shall perform in accordance process needs PT.XYZ logistics company. The translating process capability level determined by the company prior currently at on level 4. The capability level domain process in the EDM is level 4, while at domain APO, BAI, and MEA are on level 3 and gap on APO, BAI, and MEA. The company recommendation domain subscription APO, BAI, and MEA to increase the capabilities of the rate review process to achieve the targets that have can determine the company.

The RING domain of the scaffold protein Ste5 adopts a molten globular character with high thermal and chemical stability.

PubMed

Walczak, Michal J; Samatanga, Brighton; van Drogen, Frank; Peter, Matthias; Jelesarov, Ilian; Wider, Gerhard

2014-01-27

Ste5 is a scaffold protein that controls the pheromone response of the MAP-kinase cascade in yeast cells. Upon pheromone stimulation, Ste5 (through its RING-H2 domain) interacts with the β and γ subunits of an activated heterodimeric G protein and promotes activation of the MAP-kinase cascade. With structural and biophysical studies, we show that the Ste5 RING-H2 domain exists as a molten globule under native buffer conditions, in yeast extracts, and even in denaturing conditions containing urea (7 M). Furthermore, it exhibits high thermal stability in native conditions. Binding of the Ste5 RING-H2 domain to the physiological Gβ/γ (Ste4/Ste18) ligand is accompanied by a conformational transition into a better folded, more globular structure. This study reveals novel insights into the folding mechanism and recruitment of binding partners by the Ste5 RING-H2 domain. We speculate that many RING domains may share a similar mechanism of substrate recognition and molten-globule-like character. Copyright © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Substrate-specifying determinants of the nucleotide pyrophosphatases/phosphodiesterases NPP1 and NPP2

PubMed Central

2004-01-01

The nucleotide pyrophosphatases/phosphodiesterases NPP1 and NPP2/autotaxin are structurally related eukaryotic ecto-enzymes, but display a very different substrate specificity. NPP1 releases nucleoside 5′-monophosphates from various nucleotides, whereas NPP2 mainly functions as a lysophospholipase D. We have used a domain-swapping approach to map substrate-specifying determinants of NPP1 and NPP2. The catalytic domain of NPP1 fused to the N- and C-terminal domains of NPP2 was hyperactive as a nucleotide phosphodiesterase, but did not show any lysophospholipase D activity. In contrast, chimaeras of the catalytic domain of NPP2 and the N- and/or C-terminal domains of NPP1 were completely inactive. These data indicate that the catalytic domain as well as both extremities of NPP2 contain lysophospholipid-specifying sequences. Within the catalytic domain of NPP1 and NPP2, we have mapped residues close to the catalytic site that determine the activities towards nucleotides and lysophospholipids. We also show that the conserved Gly/Phe-Xaa-Gly-Xaa-Xaa-Gly (G/FXGXXG) motif near the catalytic site is required for metal binding, but is not involved in substrate-specification. Our data suggest that the distinct activities of NPP1 and NPP2 stem from multiple differences throughout the polypeptide chain. PMID:15096095

Cloning and characterization of GETS-1, a goldfish Ets family member that functions as a transcriptional repressor in muscle.

PubMed

Goldman, D; Sapru, M K; Stewart, S; Plotkin, J; Libermann, T A; Wasylyk, B; Guan, K

1998-10-15

An Ets transcription factor family member, GETS-1, was cloned from a goldfish retina cDNA library. GETS-1 contains a conserved Ets DNA-binding domain at its N-terminus and is most similar to ternary complex factor (TCF) serum-response-factor protein-1a (SAP-1a). GETS-1 is expressed in many tissues, but is enriched in retina and brain. As with the TCFs SAP-1a and ets-related protein (ERP), overexpression of the GETS-1 promoter suppresses nicotinic acetylcholine receptor epsilon-subunit gene expression in cultured muscle cells. A consensus Ets binding site sequence in the promoter of the epsilon-subunit gene is required for GETS-1-mediated repression. GETS-1 repressor activity is abrogated by overexpression of an activated Ras/mitogen-activated protein kinase (MAP kinase) or by mutation of Ser-405, a MAP kinase phosphorylation site in GETS-1. Fusion proteins created between GETS-1 and the Gal4 DNA-binding domain show that, like other TCFs, GETS-1 contains a C-terminal activation domain that is activated by a Ras/MAP kinase signalling cascade. Interestingly, mutation of Ser-405 located within this activation domain abrogated transcriptional activation of the fusion protein.

Mapping rift domains within an inverted hyperextended rift system: The role of rift inheritance in controlling the present-day structure of the North Iberian margin (Bay of Biscay)

NASA Astrophysics Data System (ADS)

Cadenas, Patricia; Fernández-Viejo, Gabriela; Álvarez-Pulgar, Javier; Tugend, Julie; Manatschal, Gianreto; Minshull, Tim

2017-04-01

This study presents a new rift domain map in the central and western North Iberian margin, in the southern Bay of Biscay. This margin was structured during polyphase Triassic to Lower Cretaceous rifting events which led to hyperextension and exhumation and the formation of oceanic crust during a short-lived seafloor spreading period. Extension was halted due to the Alpine convergence between the Iberian and the European plates which led to the formation of the Cantabrian-Pyrenean orogen during the Cenozoic. In the Bay of Biscay, while the northern Biscay margin was slightly inverted, the North Iberian margin, which is at present-day part of the western branch of the Alpine belt together with the Cantabrian Mountains, exhibits several degrees of compressional reactivation. This makes this area a natural laboratory to study the influence of rift inheritance into the inversion of a passive margin. Relying on the interpretation of geological and geophysical data and the integration of wide-angle results, we have mapped five rift domains, corresponding to the proximal, necking, hyperthinned, exhumed mantle, and oceanic domains. One of the main outcomes of this work is the identification of the Asturian Basin as part of a hyperthinned domain bounded to the north by the Le Danois basement high. We interpret Le Danois High as a rift-related crustal block inherited from the margin structure. Our results suggest that the inherited rift architecture controlled the subsequent compressional reactivation. The hyperextended domains within the abyssal plain focused most of the compression resulting in the development of an accretionary wedge and the underthrusting of part of these distal domains beneath the margin. The presence of the Le Danois continental block added complexity, conditioning the inversion undergone by the Asturian Basin. This residual block of less thinned continental crust acted as a local buttress hampering further compressional reactivation within the platform and the inner basin, which were only slightly inverted and uplifted passively due to the underthrusting of the hyperextended domains beneath Le Danois High. The new inverted rift domain map adds some constraints to support kinematic reconstructions and confine palinspatic restorations of the inverted rifted margin. Furthermore, it provides more insights to comprehend the strain partitioning within the Bay of Biscay-Pyrenean inverted hyperextended rift and the broad structural variability observed in such a reduced area, arising from the strong segmentation and the obliquity between the NW-SE and WNW-ESE trending rift structures and the E-W compressional front.

Scalable Joint Segmentation and Registration Framework for Infant Brain Images.

PubMed

Dong, Pei; Wang, Li; Lin, Weili; Shen, Dinggang; Wu, Guorong

2017-03-15

The first year of life is the most dynamic and perhaps the most critical phase of postnatal brain development. The ability to accurately measure structure changes is critical in early brain development study, which highly relies on the performances of image segmentation and registration techniques. However, either infant image segmentation or registration, if deployed independently, encounters much more challenges than segmentation/registration of adult brains due to dynamic appearance change with rapid brain development. In fact, image segmentation and registration of infant images can assists each other to overcome the above challenges by using the growth trajectories (i.e., temporal correspondences) learned from a large set of training subjects with complete longitudinal data. Specifically, a one-year-old image with ground-truth tissue segmentation can be first set as the reference domain. Then, to register the infant image of a new subject at earlier age, we can estimate its tissue probability maps, i.e., with sparse patch-based multi-atlas label fusion technique, where only the training images at the respective age are considered as atlases since they have similar image appearance. Next, these probability maps can be fused as a good initialization to guide the level set segmentation. Thus, image registration between the new infant image and the reference image is free of difficulty of appearance changes, by establishing correspondences upon the reasonably segmented images. Importantly, the segmentation of new infant image can be further enhanced by propagating the much more reliable label fusion heuristics at the reference domain to the corresponding location of the new infant image via the learned growth trajectories, which brings image segmentation and registration to assist each other. It is worth noting that our joint segmentation and registration framework is also flexible to handle the registration of any two infant images even with significant age gap in the first year of life, by linking their joint segmentation and registration through the reference domain. Thus, our proposed joint segmentation and registration method is scalable to various registration tasks in early brain development studies. Promising segmentation and registration results have been achieved for infant brain MR images aged from 2-week-old to 1-year-old, indicating the applicability of our method in early brain development study.

A comparison of two conformal mapping techniques applied to an aerobrake body

NASA Technical Reports Server (NTRS)

Hommel, Mark J.

1987-01-01

Conformal mapping is a classical technique which has been utilized for solving problems in aerodynamics and hydrodynamics. Conformal mapping has been successfully applied in the construction of grids around airfoils, engine inlets and other aircraft configurations. Conformal mapping techniques were applied to an aerobrake body having an axis of symmetry. Two different approaches were utilized: (1) Karman-Trefftz transformation; and (2) Point Wise Schwarz Christoffel transformation. In both cases, the aerobrake body was mapped onto a near circle, and a grid was generated in the mapped plane. The mapped body and grid were then mapped back into physical space and the properties of the associated grids were examined. Advantages and disadvantages of both approaches are discussed.

Mapping piezoelectric response in nanomaterials using a dedicated non-destructive scanning probe technique.

PubMed

Calahorra, Yonatan; Smith, Michael; Datta, Anuja; Benisty, Hadas; Kar-Narayan, Sohini

2017-12-14

There has been tremendous interest in piezoelectricity at the nanoscale, for example in nanowires and nanofibers where piezoelectric properties may be enhanced or controllably tuned, thus necessitating robust characterization techniques of piezoelectric response in nanomaterials. Piezo-response force microscopy (PFM) is a well-established scanning probe technique routinely used to image piezoelectric/ferroelectric domains in thin films, however, its applicability to nanoscale objects is limited due to the requirement for physical contact with an atomic force microscope (AFM) tip that may cause dislocation or damage, particularly to soft materials, during scanning. Here we report a non-destructive PFM (ND-PFM) technique wherein the tip is oscillated into "discontinuous" contact during scanning, while applying an AC bias between tip and sample and extracting the piezoelectric response for each contact point by monitoring the resulting localized deformation at the AC frequency. ND-PFM is successfully applied to soft polymeric (poly-l-lactic acid) nanowires, as well as hard ceramic (barium zirconate titanate-barium calcium titanate) nanowires, both previously inaccessible by conventional PFM. Our ND-PFM technique is versatile and compatible with commercial AFMs, and can be used to correlate piezoelectric properties of nanomaterials with their microstructural features thus overcoming key characterisation challenges in the field.

Deformation Mechanisms and Formability Window for As-Cast Mg-6Al-2Ca-1Sn-0.3Sr Alloy (MRI 230D)

NASA Astrophysics Data System (ADS)

Suresh, Kalidass; Pitcheswara Rao, Kamineni; Chalasani, Dharmendra; Yellapregada Venkata Rama Krishna, Prasad; Hort, Norbert; Dieringa, Hajo

2018-03-01

The hot deformation characteristics of MRI 230D alloy have been evaluated in the temperature range 260-500 °C and strain rate range 0.0003-10 s-1, on the basis of processing map. The processing map exhibited two domains in the ranges: (1) 300-370 °C and 0.0003-0.001 s-1 and (2) 370-480 °C and 0.0003-0.1 s-1. Dynamic recrystallization occurs in the both domains with basal slip dominating in the first domain along with climb as recovery process and second-order pyramidal slip dominating in the second with the recovery by cross-slip. In Domains (1) and (2), the apparent activation energy values estimated using the kinetic rate equation are 143 and 206 kJ/mole, respectively, the first one being close to that for lattice self-diffusion confirming climb. It is recommended that the alloy is best processed at 450 °C and strain rates less than 0.1 s-1, where non-basal slip and cross-slip occur extensively to impart excellent workability. The alloy exhibits flow instability in the form of adiabatic shear band formation and flow localization at lower temperatures and higher strain rates. Forging of a cup-shaped component was performed under various conditions, and the results validated the predictions of the processing map on the workability domains as well as the instability regimes.

Methanopyrus kandleri topoisomerase V contains three distinct AP lyase active sites in addition to the topoisomerase active site

PubMed Central

Rajan, Rakhi; Osterman, Amy; Mondragón, Alfonso

2016-01-01

Topoisomerase V (Topo-V) is the only topoisomerase with both topoisomerase and DNA repair activities. The topoisomerase activity is conferred by a small alpha-helical domain, whereas the AP lyase activity is found in a region formed by 12 tandem helix-hairpin-helix ((HhH)2) domains. Although it was known that Topo-V has multiple repair sites, only one had been mapped. Here, we show that Topo-V has three AP lyase sites. The atomic structure and Small Angle X-ray Scattering studies of a 97 kDa fragment spanning the topoisomerase and 10 (HhH)2 domains reveal that the (HhH)2 domains extend away from the topoisomerase domain. A combination of biochemical and structural observations allow the mapping of the second repair site to the junction of the 9th and 10th (HhH)2 domains. The second site is structurally similar to the first one and to the sites found in other AP lyases. The 3rd AP lyase site is located in the 12th (HhH)2 domain. The results show that Topo-V is an unusual protein: it is the only known protein with more than one (HhH)2 domain, the only known topoisomerase with dual activities and is also unique by having three AP lyase repair sites in the same polypeptide. PMID:26908655

Conformational Dynamics inside Amino-Terminal Disease Hotspot of Ryanodine Receptor

PubMed Central

Zhong, Xiaowei; Liu, Ying; Zhu, Li; Meng, Xing; Wang, Ruiwu; Van Petegem, Filip; Wagenknecht, Terence; Wayne Chen, S. R.; Liu, Zheng

2013-01-01

Summary The N-terminal region of both skeletal and cardiac ryanodine receptor is a disease mutation hotspot. Recently, a crystal structure of the RyR1 fragment (residues 1-559) was solved. This N-terminal structure contains three separate domains, A, B, and C, and was docked into a central vestibule in a full-length RyR1 cryo-EM map. Here we reconstructed 3D cryo-EM structures of two GFP-tagged RyR2s with GFP inserted after residue Glu-310 and Ser-437, respectively. The structures of RyR2E310-GFP and RyR2S437-GFP displayed an extra mass on domain B and C, directly validating the predicted docking model. Next, we revealed domain movements in molecular dynamics flexible fitting models in both the closed and open state cryo-EM maps. To further probe the conformational changes, we generated FRET pairs by inserting CFP or YFP in two selected domains, FRET studies of three dual-insertion pairs and three co-expressed single-insertion pairs showed the dynamic structural changes within the N-terminal domains. PMID:24139989

On the domain of the Nelson Hamiltonian

NASA Astrophysics Data System (ADS)

Griesemer, M.; Wünsch, A.

2018-04-01

The Nelson Hamiltonian is unitarily equivalent to a Hamiltonian defined through a closed, semibounded quadratic form, the unitary transformation being explicitly known and due to Gross. In this paper, we study the mapping properties of the Gross-transform in order to characterize the regularity properties of vectors in the form domain of the Nelson Hamiltonian. Since the operator domain is a subset of the form domain, our results apply to vectors in the domain of the Hamiltonian as well. This work is a continuation of our previous work on the Fröhlich Hamiltonian.

Signatures of Pleiotropy, Economy and Convergent Evolution in a Domain-Resolved Map of Human–Virus Protein–Protein Interaction Networks

PubMed Central

Garamszegi, Sara; Franzosa, Eric A.; Xia, Yu

2013-01-01

A central challenge in host-pathogen systems biology is the elucidation of general, systems-level principles that distinguish host-pathogen interactions from within-host interactions. Current analyses of host-pathogen and within-host protein-protein interaction networks are largely limited by their resolution, treating proteins as nodes and interactions as edges. Here, we construct a domain-resolved map of human-virus and within-human protein-protein interaction networks by annotating protein interactions with high-coverage, high-accuracy, domain-centric interaction mechanisms: (1) domain-domain interactions, in which a domain in one protein binds to a domain in a second protein, and (2) domain-motif interactions, in which a domain in one protein binds to a short, linear peptide motif in a second protein. Analysis of these domain-resolved networks reveals, for the first time, significant mechanistic differences between virus-human and within-human interactions at the resolution of single domains. While human proteins tend to compete with each other for domain binding sites by means of sequence similarity, viral proteins tend to compete with human proteins for domain binding sites in the absence of sequence similarity. Independent of their previously established preference for targeting human protein hubs, viral proteins also preferentially target human proteins containing linear motif-binding domains. Compared to human proteins, viral proteins participate in more domain-motif interactions, target more unique linear motif-binding domains per residue, and contain more unique linear motifs per residue. Together, these results suggest that viruses surmount genome size constraints by convergently evolving multiple short linear motifs in order to effectively mimic, hijack, and manipulate complex host processes for their survival. Our domain-resolved analyses reveal unique signatures of pleiotropy, economy, and convergent evolution in viral-host interactions that are otherwise hidden in the traditional binary network, highlighting the power and necessity of high-resolution approaches in host-pathogen systems biology. PMID:24339775

Signatures of pleiotropy, economy and convergent evolution in a domain-resolved map of human-virus protein-protein interaction networks.

PubMed

Garamszegi, Sara; Franzosa, Eric A; Xia, Yu

2013-01-01

A central challenge in host-pathogen systems biology is the elucidation of general, systems-level principles that distinguish host-pathogen interactions from within-host interactions. Current analyses of host-pathogen and within-host protein-protein interaction networks are largely limited by their resolution, treating proteins as nodes and interactions as edges. Here, we construct a domain-resolved map of human-virus and within-human protein-protein interaction networks by annotating protein interactions with high-coverage, high-accuracy, domain-centric interaction mechanisms: (1) domain-domain interactions, in which a domain in one protein binds to a domain in a second protein, and (2) domain-motif interactions, in which a domain in one protein binds to a short, linear peptide motif in a second protein. Analysis of these domain-resolved networks reveals, for the first time, significant mechanistic differences between virus-human and within-human interactions at the resolution of single domains. While human proteins tend to compete with each other for domain binding sites by means of sequence similarity, viral proteins tend to compete with human proteins for domain binding sites in the absence of sequence similarity. Independent of their previously established preference for targeting human protein hubs, viral proteins also preferentially target human proteins containing linear motif-binding domains. Compared to human proteins, viral proteins participate in more domain-motif interactions, target more unique linear motif-binding domains per residue, and contain more unique linear motifs per residue. Together, these results suggest that viruses surmount genome size constraints by convergently evolving multiple short linear motifs in order to effectively mimic, hijack, and manipulate complex host processes for their survival. Our domain-resolved analyses reveal unique signatures of pleiotropy, economy, and convergent evolution in viral-host interactions that are otherwise hidden in the traditional binary network, highlighting the power and necessity of high-resolution approaches in host-pathogen systems biology.

Functional Connectivity of Resting Hemodynamic Signals in Submillimeter Orientation Columns of the Visual Cortex.

PubMed

Vasireddi, Anil K; Vazquez, Alberto L; Whitney, David E; Fukuda, Mitsuhiro; Kim, Seong-Gi

2016-09-07

Resting-state functional magnetic resonance imaging has been increasingly used for examining connectivity across brain regions. The spatial scale by which hemodynamic imaging can resolve functional connections at rest remains unknown. To examine this issue, deoxyhemoglobin-weighted intrinsic optical imaging data were acquired from the visual cortex of lightly anesthetized ferrets. The neural activity of orientation domains, which span a distance of 0.7-0.8 mm, has been shown to be correlated during evoked activity and at rest. We performed separate analyses to assess the degree to which the spatial and temporal characteristics of spontaneous hemodynamic signals depend on the known functional organization of orientation columns. As a control, artificial orientation column maps were generated. Spatially, resting hemodynamic patterns showed a higher spatial resemblance to iso-orientation maps than artificially generated maps. Temporally, a correlation analysis was used to establish whether iso-orientation domains are more correlated than orthogonal orientation domains. After accounting for a significant decrease in correlation as a function of distance, a small but significant temporal correlation between iso-orientation domains was found, which decreased with increasing difference in orientation preference. This dependence was abolished when using artificially synthetized orientation maps. Finally, the temporal correlation coefficient as a function of orientation difference at rest showed a correspondence with that calculated during visual stimulation suggesting that the strength of resting connectivity is related to the strength of the visual stimulation response. Our results suggest that temporal coherence of hemodynamic signals measured by optical imaging of intrinsic signals exists at a submillimeter columnar scale in resting state.

Electron Energy Loss Spectroscopy imaging of surface plasmons at the nanometer scale.

PubMed

Colliex, Christian; Kociak, Mathieu; Stéphan, Odile

2016-03-01

Since their first realization, electron microscopes have demonstrated their unique ability to map with highest spatial resolution (sub-atomic in most recent instruments) the position of atoms as a consequence of the strong scattering of the incident high energy electrons by the nuclei of the material under investigation. When interacting with the electron clouds either on atomic orbitals or delocalized over the specimen, the associated energy transfer, measured and analyzed as an energy loss (Electron Energy Loss Spectroscopy) gives access to analytical properties (atom identification, electron states symmetry and localization). In the moderate energy-loss domain (corresponding to an optical spectral domain from the infrared (IR) to the rather far ultra violet (UV), EELS spectra exhibit characteristic collective excitations of the rather-free electron gas, known as plasmons. Boundary conditions, such as surfaces and/or interfaces between metallic and dielectric media, generate localized surface charge oscillations, surface plasmons (SP), which are associated with confined electric fields. This domain of research has been extraordinarily revived over the past few years as a consequence of the burst of interest for structures and devices guiding, enhancing and controlling light at the sub-wavelength scale. The present review focuses on the study of these surface plasmons with an electron microscopy-based approach which associates spectroscopy and mapping at the level of a single and well-defined nano-object, typically at the nanometer scale i.e. much improved with respect to standard, and even near-field, optical techniques. After calling to mind some early studies, we will briefly mention a few basic aspects of the required instrumentation and associated theoretical tools to interpret the very rich data sets recorded with the latest generation of (Scanning)TEM microscopes. The following paragraphs will review in more detail the results obtained on simple planar and spherical surfaces (or interfaces), extending then to more complex geometries isolated and in interaction, thus establishing basic rules from the classical to the quantum domain. A few hints towards application domains and prospective fields rich of interest will finally be indicated, confirming the demonstrated key role of electron-beam nanoplasmonics, the more as an yet-enhanced energy resolution down to the 10meV comes on the verge of current access. Copyright © 2015 Elsevier B.V. All rights reserved.

SH3 interactome conserves general function over specific form

PubMed Central

Xin, Xiaofeng; Gfeller, David; Cheng, Jackie; Tonikian, Raffi; Sun, Lin; Guo, Ailan; Lopez, Lianet; Pavlenco, Alevtina; Akintobi, Adenrele; Zhang, Yingnan; Rual, Jean-François; Currell, Bridget; Seshagiri, Somasekar; Hao, Tong; Yang, Xinping; Shen, Yun A; Salehi-Ashtiani, Kourosh; Li, Jingjing; Cheng, Aaron T; Bouamalay, Dryden; Lugari, Adrien; Hill, David E; Grimes, Mark L; Drubin, David G; Grant, Barth D; Vidal, Marc; Boone, Charles; Sidhu, Sachdev S; Bader, Gary D

2013-01-01

Src homology 3 (SH3) domains bind peptides to mediate protein–protein interactions that assemble and regulate dynamic biological processes. We surveyed the repertoire of SH3 binding specificity using peptide phage display in a metazoan, the worm Caenorhabditis elegans, and discovered that it structurally mirrors that of the budding yeast Saccharomyces cerevisiae. We then mapped the worm SH3 interactome using stringent yeast two-hybrid and compared it with the equivalent map for yeast. We found that the worm SH3 interactome resembles the analogous yeast network because it is significantly enriched for proteins with roles in endocytosis. Nevertheless, orthologous SH3 domain-mediated interactions are highly rewired. Our results suggest a model of network evolution where general function of the SH3 domain network is conserved over its specific form. PMID:23549480

Semantics-informed geological maps: Conceptual modeling and knowledge encoding

NASA Astrophysics Data System (ADS)

Lombardo, Vincenzo; Piana, Fabrizio; Mimmo, Dario

2018-07-01

This paper introduces a novel, semantics-informed geologic mapping process, whose application domain is the production of a synthetic geologic map of a large administrative region. A number of approaches concerning the expression of geologic knowledge through UML schemata and ontologies have been around for more than a decade. These approaches have yielded resources that concern specific domains, such as, e.g., lithology. We develop a conceptual model that aims at building a digital encoding of several domains of geologic knowledge, in order to support the interoperability of the sources. We apply the devised terminological base to the classification of the elements of a geologic map of the Italian Western Alps and northern Apennines (Piemonte region). The digitally encoded knowledge base is a merged set of ontologies, called OntoGeonous. The encoding process identifies the objects of the semantic encoding, the geologic units, gathers the relevant information about such objects from authoritative resources, such as GeoSciML (giving priority to the application schemata reported in the INSPIRE Encoding Cookbook), and expresses the statements by means of axioms encoded in the Web Ontology Language (OWL). To support interoperability, OntoGeonous interlinks the general concepts by referring to the upper part level of ontology SWEET (developed by NASA), and imports knowledge that is already encoded in ontological format (e.g., ontology Simple Lithology). Machine-readable knowledge allows for consistency checking and for classification of the geological map data through algorithms of automatic reasoning.

Fate-mapping the mammalian hindbrain: segmental origins of vestibular projection neurons assessed using rhombomere-specific Hoxa2 enhancer elements in the mouse embryo.

PubMed

Pasqualetti, Massimo; Díaz, Carmen; Renaud, Jean-Sébastien; Rijli, Filippo M; Glover, Joel C

2007-09-05

As a step toward generating a fate map of identified neuron populations in the mammalian hindbrain, we assessed the contributions of individual rhombomeres to the vestibular nuclear complex, a major sensorimotor area that spans the entire rhombencephalon. Transgenic mice harboring either the lacZ or the enhanced green fluorescent protein reporter genes under the transcriptional control of rhombomere-specific Hoxa2 enhancer elements were used to visualize rhombomere-derived domains. We labeled functionally identifiable vestibular projection neuron groups retrogradely with conjugated dextran-amines at successive embryonic stages and obtained developmental fate maps through direct comparison with the rhombomere-derived domains in the same embryos. The fate maps show that each vestibular neuron group derives from a unique rostrocaudal domain that is relatively stable developmentally, suggesting that anteroposterior migration is not a major contributor to the rostrocaudal patterning of the vestibular system. Most of the groups are multisegmental in origin, and each rhombomere is fated to give rise to two or more vestibular projection neuron types, in a complex pattern that is not segmentally iterated. Comparison with studies in the chicken embryo shows that the rostrocaudal patterning of identified vestibular projection neuron groups is generally well conserved between avians and mammalians but that significant species-specific differences exist in the rostrocaudal limits of particular groups. This mammalian hindbrain fate map can be used as the basis for targeting genetic manipulation to specific subpopulations of vestibular projection neurons.

Site-specific microtubule-associated protein 4 dephosphorylation causes microtubule network densification in pressure overload cardiac hypertrophy.

PubMed

Chinnakkannu, Panneerselvam; Samanna, Venkatesababa; Cheng, Guangmao; Ablonczy, Zsolt; Baicu, Catalin F; Bethard, Jennifer R; Menick, Donald R; Kuppuswamy, Dhandapani; Cooper, George

2010-07-09

In severe pressure overload-induced cardiac hypertrophy, a dense, stabilized microtubule network forms that interferes with cardiocyte contraction and microtubule-based transport. This is associated with persistent transcriptional up-regulation of cardiac alpha- and beta-tubulin and microtubule-stabilizing microtubule-associated protein 4 (MAP4). There is also extensive microtubule decoration by MAP4, suggesting greater MAP4 affinity for microtubules. Because the major determinant of this affinity is site-specific MAP4 dephosphorylation, we characterized this in hypertrophied myocardium and then assessed the functional significance of each dephosphorylation site found by mimicking it in normal cardiocytes. We first isolated MAP4 from normal and pressure overload-hypertrophied feline myocardium; volume-overloaded myocardium, which has an equal degree and duration of hypertrophy but normal functional and cytoskeletal properties, served as a control for any nonspecific growth-related effects. After cloning cDNA-encoding feline MAP4 and obtaining its deduced amino acid sequence, we characterized by mass spectrometry any site-specific MAP4 dephosphorylation. Solely in pressure overload-hypertrophied myocardium, we identified striking MAP4 dephosphorylation at Ser-472 in the MAP4 N-terminal projection domain and at Ser-924 and Ser-1056 in the assembly-promoting region of the C-terminal microtubule-binding domain. Site-directed mutagenesis of MAP4 cDNA was then used to switch each serine to non-phosphorylatable alanine. Wild-type and mutated cDNAs were used to construct adenoviruses; microtubule network density, stability, and MAP4 decoration were assessed in normal cardiocytes following an equivalent level of MAP4 expression. The Ser-924 --> Ala MAP4 mutant produced a microtubule phenotype indistinguishable from that seen in pressure overload hypertrophy, such that Ser-924 MAP4 dephosphorylation during pressure overload hypertrophy may be central to this cytoskeletal abnormality.

Hydrogeological Characterization of the Upper Camp Bird III Rock Glacier in the San Juan Mountains, Colorado Using Electromagnetic Induction

NASA Astrophysics Data System (ADS)

Granados-Aguilar, R.; Giardino, J. R.; Everett, M. E.; Pondthai, P.; Ramsey, C. E.; Mmasa, D.; Witek, M.; Rodriguez, R.

2017-12-01

Global change is the set of variations in environmental conditions that significantly impact the Earth systems. Climate, sea level, land-use/land-cover, and atmospheric composition changes are the most recognized environmental global changes. Impacts of climatic variability can include decreased rainfall, snowpack, shorter snow seasons, and changes in the timing, frequency, and intensity of precipitation events in some areas of the world, whereas other regions can suffer from the opposite effects leading to events such as landslides, flooding and extraordinary snowfall. The proposed research intends to provide a characterization of the internal structure, including water storages, pathways, and thresholds, as well as an estimation of the volume of ice stored within a rock glacier to evaluate its potential as a freshwater resources. The area of study corresponds to the third level of Camp Bird Mine in Ouray, Colorado. The tongue-shaped active rock glacier of interest, Upper Camp Bird III, has not been previously studied in detail. The predominant lithologies in the study area are Mesozoic and Cenozoic. Orogenic events caused alteration of sedimentary and intrusive igneous rock as mineral rich, hydrothermal fluids deposited economically valuable minerals in the region. Traditional geological and geomorphological mapping techniques will be complemented with the use of unmanned aerial vehicles (UAV). To obtain a detailed representation of the internal structure and determine the boundaries between resistive (rocks, sediment, and ice) and conductive materials (water and ore deposits) of the rock glacier, time-domain and frequency-domain methods will be implemented. The G-TEM by Geonics Ltd. is an innovative controlled-source time-domain electromagnetic induction system. Using the G-TEM, the distribution of electrical conductivity in the subsurface can be mapped in order to characterize the internal structure of the rock glacier from 5-10 m depth and below. The EM Profiler is a frequency-domain electromagnetic induction system that will be used for the investigation of the uppermost layers of the rock glacier. For the proposed research, the use of two different systems will provide continuity across the data sets and will help validate the measurements recorded with the new equipment.

Using Concept Maps to Monitor Knowledge Structure Changes in a Science Classroom

ERIC Educational Resources Information Center

Cook, Leah J.

2017-01-01

The aim of this research is to determine what differences may exist in students' structural knowledge while using a variety of concept mapping assessments. A concept map can be used as an assessment which connects concepts in a knowledge domain. A single assessment may not be powerful enough to establish how students' new knowledge relates to…

A Study to Determine the Contribution Made by Concept Maps to a Computer Architecture and Organization Course

ERIC Educational Resources Information Center

Aydogan, Tuncay; Ergun, Serap

2016-01-01

Concept mapping is a method of graphical learning that can be beneficial as a study method for concept linking and organization. Concept maps, which provide an elegant, easily understood representation of an expert's domain knowledge, are tools for organizing and representing knowledge. These tools have been used in educational environments to…

Topic Maps: Adopting User-Centred Indexing Technologies in Course Management Systems

ERIC Educational Resources Information Center

Venkatesh, Vivek; Shaw, Steven; Dicks, Dennis; Lowerison, Gretchen; Zhang, Dai; Sanjakdar, Roukana

2007-01-01

This article provides an empirical evaluation of an indexing technology, topic maps (ISO 13250), in the context of an academic task in a higher education context. Topic maps are a form of indexing that define and display the interrelationships between various topics in a given domain, as well as anchor these topics to specific resources that help…

Cognitive Mapping Techniques: Implications for Research in Engineering and Technology Education

ERIC Educational Resources Information Center

Dixon, Raymond A.; Lammi, Matthew

2014-01-01

The primary goal of this paper is to present the theoretical basis and application of two types of cognitive maps, concept map and mind map, and explain how they can be used by educational researchers in engineering design research. Cognitive mapping techniques can be useful to researchers as they study students' problem solving strategies…

Hot Deformation Behavior and Intrinsic Workability of Carbon Nanotube-Aluminum Reinforced ZA27 Composites

NASA Astrophysics Data System (ADS)

Liu, Yang; Geng, Cong; Zhu, Yunke; Peng, Jinfeng; Xu, Junrui

2017-04-01

Using a controlled thermal simulator system, hybrid carbon nanotube-aluminum reinforced ZA27 composites were subjected to hot compression testing in the temperature range of 473-523 K with strain rates of 0.01-10 s-1. Based on experimental results, a developed-flow stress model was established using a constitutive equation coupled with strain to describe strain softening arising from dynamic recrystallization. The intrinsic workability was further investigated by constructing three-dimensional (3D) processing maps aided by optical observations of microstructures. The 3D processing maps were constructed based on a dynamic model of materials to delineate variations in the efficiency of power dissipation and flow instability domains. The instability domains exhibited adiabatic shear band and flow localization, which need to be prevented during hot processing. The recommended domain is predicated to be within the temperature range 550-590 K and strain rate range 0.01-0.35 s-1. In this state, the main softening mechanism is dynamic recrystallization. The results from processing maps agree well with the microstructure observations.

Quasipolynomial generalization of Lotka-Volterra mappings

NASA Astrophysics Data System (ADS)

Hernández-Bermejo, Benito; Brenig, Léon

2002-07-01

In recent years, it has been shown that Lotka-Volterra mappings constitute a valuable tool from both the theoretical and the applied points of view, with developments in very diverse fields such as physics, population dynamics, chemistry and economy. The purpose of this work is to demonstrate that many of the most important ideas and algebraic methods that constitute the basis of the quasipolynomial formalism (originally conceived for the analysis of ordinary differential equations) can be extended into the mapping domain. The extension of the formalism into the discrete-time context is remarkable as far as the quasipolynomial methodology had never been shown to be applicable beyond the differential case. It will be demonstrated that Lotka-Volterra mappings play a central role in the quasipolynomial formalism for the discrete-time case. Moreover, the extension of the formalism into the discrete-time domain allows a significant generalization of Lotka-Volterra mappings as well as a whole transfer of algebraic methods into the discrete-time context. The result is a novel and more general conceptual framework for the understanding of Lotka-Volterra mappings as well as a new range of possibilities that become open not only for the theoretical analysis of Lotka-Volterra mappings and their generalizations, but also for the development of new applications.

Geomorphic domains and linear features on Landsat images, Circle Quadrangle, Alaska

USGS Publications Warehouse

Simpson, S.L.

1984-01-01

A remote sensing study using Landsat images was undertaken as part of the Alaska Mineral Resource Assessment Program (AMRAP). Geomorphic domains A and B, identified on enhanced Landsat images, divide Circle quadrangle south of Tintina fault zone into two regional areas having major differences in surface characteristics. Domain A is a roughly rectangular, northeast-trending area of relatively low relief and simple, widely spaced drainages, except where igneous rocks are exposed. In contrast, domain B, which bounds two sides of domain A, is more intricately dissected showing abrupt changes in slope and relatively high relief. The northwestern part of geomorphic domain A includes a previously mapped tectonostratigraphic terrane. The southeastern boundary of domain A occurs entirely within the adjoining tectonostratigraphic terrane. The sharp geomorphic contrast along the southeastern boundary of domain A and the existence of known faults along this boundary suggest that the southeastern part of domain A may be a subdivision of the adjoining terrane. Detailed field studies would be necessary to determine the characteristics of the subdivision. Domain B appears to be divisible into large areas of different geomorphic terrains by east-northeast-trending curvilinear lines drawn on Landsat images. Segments of two of these lines correlate with parts of boundaries of mapped tectonostratigraphic terranes. On Landsat images prominent north-trending lineaments together with the curvilinear lines form a large-scale regional pattern that is transected by mapped north-northeast-trending high-angle faults. The lineaments indicate possible lithlogic variations and/or structural boundaries. A statistical strike-frequency analysis of the linear features data for Circle quadrangle shows that northeast-trending linear features predominate throughout, and that most northwest-trending linear features are found south of Tintina fault zone. A major trend interval of N.64-72E. in the linear feature data, corresponds to the strike of foliations in metamorphic rocks and magnetic anomalies reflecting compositional variations suggesting that most linear features in the southern part of the quadrangle probably are related to lithologic variations brought about by folding and foliation of metamorphic rocks. A second important trend interval, N.14-35E., may be related to thrusting south of the Tintina fault zone, as high concentrations of linear features within this interval are found in areas of mapped thrusts. Low concentrations of linear features are found in areas of most igneous intrusives. High concentrations of linear features do not correspond to areas of mineralization in any consistent or significant way that would allow concentration patterns to be easily used as an aid in locating areas of mineralization. The results of this remote sensing study indicate that there are several possibly important areas where further detailed studies are warranted.

Historical shoreline mapping (I): improving techniques and reducing positioning errors

USGS Publications Warehouse

Thieler, E. Robert; Danforth, William W.

1994-01-01

A critical need exists among coastal researchers and policy-makers for a precise method to obtain shoreline positions from historical maps and aerial photographs. A number of methods that vary widely in approach and accuracy have been developed to meet this need. None of the existing methods, however, address the entire range of cartographic and photogrammetric techniques required for accurate coastal mapping. Thus, their application to many typical shoreline mapping problems is limited. In addition, no shoreline mapping technique provides an adequate basis for quantifying the many errors inherent in shoreline mapping using maps and air photos. As a result, current assessments of errors in air photo mapping techniques generally (and falsely) assume that errors in shoreline positions are represented by the sum of a series of worst-case assumptions about digitizer operator resolution and ground control accuracy. These assessments also ignore altogether other errors that commonly approach ground distances of 10 m. This paper provides a conceptual and analytical framework for improved methods of extracting geographic data from maps and aerial photographs. We also present a new approach to shoreline mapping using air photos that revises and extends a number of photogrammetric techniques. These techniques include (1) developing spatially and temporally overlapping control networks for large groups of photos; (2) digitizing air photos for use in shoreline mapping; (3) preprocessing digitized photos to remove lens distortion and film deformation effects; (4) simultaneous aerotriangulation of large groups of spatially and temporally overlapping photos; and (5) using a single-ray intersection technique to determine geographic shoreline coordinates and express the horizontal and vertical error associated with a given digitized shoreline. As long as historical maps and air photos are used in studies of shoreline change, there will be a considerable amount of error (on the order of several meters) present in shoreline position and rate-of- change calculations. The techniques presented in this paper, however, provide a means to reduce and quantify these errors so that realistic assessments of the technological noise (as opposed to geological noise) in geographic shoreline positions can be made.

Remote sensing of tropospheric turbulence using GPS radio occultation

NASA Astrophysics Data System (ADS)

Shume, Esayas; Ao, Chi

2016-07-01

Radio occultation (RO) measurements are sensitive to the small-scale irregularities in the atmosphere. In this study, we present a new technique to estimate tropospheric turbulence strength (namely, scintillation index) by analyzing RO amplitude fluctuations in impact parameter domain. GPS RO observations from the COSMIC (Constellation Observing System for Meteorology, Ionosphere, and Climate) satellites enabled us to calculate global maps of scintillation measures, revealing the seasonal, latitudinal, and longitudinal characteristics of the turbulent troposphere. Such information are both difficult and expensive to obtain especially over the oceans. To verify our approach, simulation experiments using the multiple phase screen (MPS) method were conducted. The results show that scintillation indices inferred from the MPS simulations are in good agreement with scintillation measures estimated from COSMIC observations.

Thermal contact through a two-temperature kinetic Ising chain

NASA Astrophysics Data System (ADS)

Bauer, M.; Cornu, F.

2018-05-01

We consider a model for thermal contact through a diathermal interface between two macroscopic bodies at different temperatures: an Ising spin chain with nearest neighbor interactions is endowed with a Glauber dynamics with different temperatures and kinetic parameters on alternating sites. The inhomogeneity of the kinetic parameter is a novelty with respect to the model of Racz and Zia (1994 Phys. Rev. E 49 139), and we exhibit its influence upon the stationary non equilibrium values of the two-spin correlations at any distance. By mapping to the dynamics of spin domain walls and using free fermion techniques, we determine the scaled generating function for the cumulants of the exchanged heat amounts per unit of time in the long time limit.

Characterization of stickiness by means of recurrence.

PubMed

Zou, Yong; Thiel, Marco; Romano, M Carmen; Kurths, Jürgen

2007-12-01

We propose recurrence plots (RPs) to characterize the stickiness of a typical area-preserving map with coexisting chaotic and regular orbits. The difference of the recurrence properties between quasiperiodic and chaotic orbits is revisited, which helps to understand the complex patterns of the corresponding RPs. Moreover, several measures from the recurrence quantification analysis are used to quantify these patterns. Among these measures, the recurrence rate, quantifying the percentage of black points in the plot, is applied to characterize the stickiness of a typical chaotic orbit. The advantage of the recurrence based method in comparison to other standard techniques is that it is possible to distinguish between quasiperiodic and chaotic orbits that are temporarily trapped in a sticky domain, from very short trajectories.

Combining textual and visual information for image retrieval in the medical domain.

PubMed

Gkoufas, Yiannis; Morou, Anna; Kalamboukis, Theodore

2011-01-01

In this article we have assembled the experience obtained from our participation in the imageCLEF evaluation task over the past two years. Exploitation on the use of linear combinations for image retrieval has been attempted by combining visual and textual sources of images. From our experiments we conclude that a mixed retrieval technique that applies both textual and visual retrieval in an interchangeably repeated manner improves the performance while overcoming the scalability limitations of visual retrieval. In particular, the mean average precision (MAP) has increased from 0.01 to 0.15 and 0.087 for 2009 and 2010 data, respectively, when content-based image retrieval (CBIR) is performed on the top 1000 results from textual retrieval based on natural language processing (NLP).

Conditional Random Field-Based Offline Map Matching for Indoor Environments

PubMed Central

Bataineh, Safaa; Bahillo, Alfonso; Díez, Luis Enrique; Onieva, Enrique; Bataineh, Ikram

2016-01-01

In this paper, we present an offline map matching technique designed for indoor localization systems based on conditional random fields (CRF). The proposed algorithm can refine the results of existing indoor localization systems and match them with the map, using loose coupling between the existing localization system and the proposed map matching technique. The purpose of this research is to investigate the efficiency of using the CRF technique in offline map matching problems for different scenarios and parameters. The algorithm was applied to several real and simulated trajectories of different lengths. The results were then refined and matched with the map using the CRF algorithm. PMID:27537892

Conditional Random Field-Based Offline Map Matching for Indoor Environments.

PubMed

Bataineh, Safaa; Bahillo, Alfonso; Díez, Luis Enrique; Onieva, Enrique; Bataineh, Ikram

2016-08-16

In this paper, we present an offline map matching technique designed for indoor localization systems based on conditional random fields (CRF). The proposed algorithm can refine the results of existing indoor localization systems and match them with the map, using loose coupling between the existing localization system and the proposed map matching technique. The purpose of this research is to investigate the efficiency of using the CRF technique in offline map matching problems for different scenarios and parameters. The algorithm was applied to several real and simulated trajectories of different lengths. The results were then refined and matched with the map using the CRF algorithm.

Digital Mapping Techniques '07 - Workshop Proceedings

USGS Publications Warehouse

Soller, David R.

2008-01-01

The Digital Mapping Techniques '07 (DMT'07) workshop was attended by 85 technical experts from 49 agencies, universities, and private companies, including representatives from 27 state geological surveys. This year's meeting, the tenth in the annual series, was hosted by the South Carolina Geological Survey, from May 20-23, 2007, on the University of South Carolina campus in Columbia, South Carolina. Each DMT workshop has been coordinated by the U.S. Geological Survey's National Geologic Map Database Project and the Association of American State Geologists (AASG). As in previous year's meetings, the objective was to foster informal discussion and exchange of technical information, principally in order to develop more efficient methods for digital mapping, cartography, GIS analysis, and information management. At this meeting, oral and poster presentations and special discussion sessions emphasized: 1) methods for creating and publishing map products (here, 'publishing' includes Web-based release); 2) field data capture software and techniques, including the use of LIDAR; 3) digital cartographic techniques; 4) migration of digital maps into ArcGIS Geodatabase format; 5) analytical GIS techniques; and 6) continued development of the National Geologic Map Database.

Selective plane illumination microscopy (SPIM) with time-domain fluorescence lifetime imaging microscopy (FLIM) for volumetric measurement of cleared mouse brain samples

NASA Astrophysics Data System (ADS)

Funane, Tsukasa; Hou, Steven S.; Zoltowska, Katarzyna Marta; van Veluw, Susanne J.; Berezovska, Oksana; Kumar, Anand T. N.; Bacskai, Brian J.

2018-05-01

We have developed an imaging technique which combines selective plane illumination microscopy with time-domain fluorescence lifetime imaging microscopy (SPIM-FLIM) for three-dimensional volumetric imaging of cleared mouse brains with micro- to mesoscopic resolution. The main features of the microscope include a wavelength-adjustable pulsed laser source (Ti:sapphire) (near-infrared) laser, a BiBO frequency-doubling photonic crystal, a liquid chamber, an electrically focus-tunable lens, a cuvette based sample holder, and an air (dry) objective lens. The performance of the system was evaluated with a lifetime reference dye and micro-bead phantom measurements. Intensity and lifetime maps of three-dimensional human embryonic kidney (HEK) cell culture samples and cleared mouse brain samples expressing green fluorescent protein (GFP) (donor only) and green and red fluorescent protein [positive Förster (fluorescence) resonance energy transfer] were acquired. The results show that the SPIM-FLIM system can be used for sample sizes ranging from single cells to whole mouse organs and can serve as a powerful tool for medical and biological research.

Domain structure of BiFeO3 thin films grown on patterned SrTiO3(001) substrates

NASA Astrophysics Data System (ADS)

Nakashima, Seiji; Seto, Shota; Kurokawa, Yuta; Fujisawa, Hironori; Shimizu, Masaru

2017-10-01

Recently, new functionalities of ferroelectric domain walls (DWs) have attracted much attention. To realize novel devices using the functionalities of the DWs, techniques to introduce the DWs at arbitrary positions in the ferroelectric thin films are necessary. In this study, we have demonstrated the introduction of the DWs at arbitrary positions in epitaxial BiFeO3 (BFO) thin films using the patterned surface of the SrTiO3 (STO) single-crystal substrate. On the slope pattern of the STO surface, the in-plane orientation of BFO has changed because the in-plane orientation of BFO can be controlled by the step propagation direction of the patterned surface. From the piezoresponse scanning force microscopy and X-ray diffraction reciprocal space mapping results, charged 109° DWs have been introduced into the BFO thin film at the bottom and top of the slope pattern of the STO surface. In addition, the conductivity modulation of the positively charged DW has been observed by current-sensitive atomic force microscopy imaging.

Rapid Frequency Chirps of TAE mode due to Finite Orbit Energetic Particles

NASA Astrophysics Data System (ADS)

Berk, Herb; Wang, Ge

2013-10-01

The tip model for the TAE mode in the large aspect ratio limit, conceived by Rosenbluth et al. in the frequency domain, together with an interaction term in the frequency domain based on a map model, has been extended into the time domain. We present the formal basis for the model, starting with the Lagrangian for the particle wave interaction. We shall discuss the formal nonlinear time domain problem and the procedure that needs to obtain solutions in the adiabatic limit.

Evaluating, Comparing, and Interpreting Protein Domain Hierarchies

PubMed Central

2014-01-01

Abstract Arranging protein domain sequences hierarchically into evolutionarily divergent subgroups is important for investigating evolutionary history, for speeding up web-based similarity searches, for identifying sequence determinants of protein function, and for genome annotation. However, whether or not a particular hierarchy is optimal is often unclear, and independently constructed hierarchies for the same domain can often differ significantly. This article describes methods for statistically evaluating specific aspects of a hierarchy, for probing the criteria underlying its construction and for direct comparisons between hierarchies. Information theoretical notions are used to quantify the contributions of specific hierarchical features to the underlying statistical model. Such features include subhierarchies, sequence subgroups, individual sequences, and subgroup-associated signature patterns. Underlying properties are graphically displayed in plots of each specific feature's contributions, in heat maps of pattern residue conservation, in “contrast alignments,” and through cross-mapping of subgroups between hierarchies. Together, these approaches provide a deeper understanding of protein domain functional divergence, reveal uncertainties caused by inconsistent patterns of sequence conservation, and help resolve conflicts between competing hierarchies. PMID:24559108

3D Reconstruction of geological structures based on remote sensing data: example from Anaran anticline, Lurestan province, Zagros folds and thrust belt, Iran.

NASA Astrophysics Data System (ADS)

Snidero, M.; Amilibia, A.; Gratacos, O.; Muñoz, J. A.

2009-04-01

This work presents a methodological workflow for the 3D reconstruction of geological surfaces at regional scale, based on remote sensing data and geological maps. This workflow has been tested on the reconstruction of the Anaran anticline, located in the Zagros Fold and Thrust belt mountain front. The used remote sensing data-set is a combination of Aster and Spot images as well as a high resolution digital elevation model. A consistent spatial positioning of the complete data-set in a 3D environment is necessary to obtain satisfactory results during the reconstruction. The Aster images have been processed by the Optimum Index Factor (OIF) technique, in order to facilitate the geological mapping. By pansharpening of the resulting Aster image with the SPOT panchromatic one we obtain the final high-resolution image used during the 3D mapping. Structural data (dip data) has been acquired through the analysis of the 3D mapped geological traces. Structural analysis of the resulting data-set allows us to divide the structure in different cylindrical domains. Related plunge lines orientation has been used to project data along the structure, covering areas with little or no information. Once a satisfactory dataset has been acquired, we reconstruct a selected horizon following the dip-domain concept. By manual editing, the obtained surfaces have been adjusted to the mapped geological limits as well as to the modeled faults. With the implementation of the Discrete Smooth Interpolation (DSI) algorithm, the final surfaces have been reconstructed along the anticline. Up to date the results demonstrate that the proposed methodology is a powerful tool for 3D reconstruction of geological surfaces when working with remote sensing data, in very inaccessible areas (eg. Iran, China, Africa). It is especially useful in semiarid regions where the structure strongly controls the topography. The reconstructed surfaces clearly show the geometry in the different sectors of the structure: presence of a back thrust affecting the back limb in the southern part of the anticline, the geometry of the grabens located along the anticline crest, the crosscutting relationship in the north-south faulted zone with the main thrust, the northern dome periclinal closure.

Fusing modeling techniques to support domain analysis for reuse opportunities identification

NASA Technical Reports Server (NTRS)

Hall, Susan Main; Mcguire, Eileen

1993-01-01

Functional modeling techniques or object-oriented graphical representations, which are more useful to someone trying to understand the general design or high level requirements of a system? For a recent domain analysis effort, the answer was a fusion of popular modeling techniques of both types. By using both functional and object-oriented techniques, the analysts involved were able to lean on their experience in function oriented software development, while taking advantage of the descriptive power available in object oriented models. In addition, a base of familiar modeling methods permitted the group of mostly new domain analysts to learn the details of the domain analysis process while producing a quality product. This paper describes the background of this project and then provides a high level definition of domain analysis. The majority of this paper focuses on the modeling method developed and utilized during this analysis effort.

Application of Cross-Correlation Greens Function Along With FDTD for Fast Computation of Envelope Correlation Coefficient Over Wideband for MIMO Antennas

NASA Astrophysics Data System (ADS)

Sarkar, Debdeep; Srivastava, Kumar Vaibhav

2017-02-01

In this paper, the concept of cross-correlation Green's functions (CGF) is used in conjunction with the finite difference time domain (FDTD) technique for calculation of envelope correlation coefficient (ECC) of any arbitrary MIMO antenna system over wide frequency band. Both frequency-domain (FD) and time-domain (TD) post-processing techniques are proposed for possible application with this FDTD-CGF scheme. The FDTD-CGF time-domain (FDTD-CGF-TD) scheme utilizes time-domain signal processing methods and exhibits significant reduction in ECC computation time as compared to the FDTD-CGF frequency domain (FDTD-CGF-FD) scheme, for high frequency-resolution requirements. The proposed FDTD-CGF based schemes can be applied for accurate and fast prediction of wideband ECC response, instead of the conventional scattering parameter based techniques which have several limitations. Numerical examples of the proposed FDTD-CGF techniques are provided for two-element MIMO systems involving thin-wire half-wavelength dipoles in parallel side-by-side as well as orthogonal arrangements. The results obtained from the FDTD-CGF techniques are compared with results from commercial electromagnetic solver Ansys HFSS, to verify the validity of proposed approach.

Mapping of non-numerical domains on space: a systematic review and meta-analysis.

PubMed

Macnamara, Anne; Keage, Hannah A D; Loetscher, Tobias

2018-02-01

The spatial numerical association of response code (SNARC) effect is characterized by low numbers mapped to the left side of space and high numbers mapped to the right side of space. In addition to numbers, SNARC-like effects have been found in non-numerical magnitude domains such as time, size, letters, luminance, and more, whereby the smaller/earlier and larger/later magnitudes are typically mapped to the left and right of space, respectively. The purpose of this systematic and meta-analytic review was to identify and summarise all empirical papers that have investigated horizontal (left-right) SNARC-like mappings using non-numerical stimuli. A systematic search was conducted using EMBASE, Medline, and PsycINFO, where 2216 publications were identified, with 57 papers meeting the inclusion criteria (representing 112 experiments). Ninety-five of these experiments were included in a meta-analysis, resulting in an overall effect size of d = .488 for a SNARC-like effect. Additional analyses revealed a significant effect size advantage for explicit instruction tasks compared with implicit instructions, yet yielded no difference for the role of expertise on SNARC-like effects. There was clear evidence for a publication bias in the field, but the impact of this bias is likely to be modest, and it is unlikely that the SNARC-like effect is a pure artefact of this bias. The similarities in the response properties for the spatial mappings of numerical and non-numerical domains support the concept of a general higher order magnitude system. Yet, further research will need to be conducted to identify all the factors modulating the strength of the spatial associations.

Structure of the PSD-95/MAP1A complex reveals a unique target recognition mode of the MAGUK GK domain.

PubMed

Xia, Yitian; Shang, Yuan; Zhang, Rongguang; Zhu, Jinwei

2017-08-10

The PSD-95 family of membrane-associated guanylate kinases (MAGUKs) are major synaptic scaffold proteins and play crucial roles in the dynamic regulation of dendritic remodelling, which is understood to be the foundation of synaptogenesis and synaptic plasticity. The guanylate kinase (GK) domain of MAGUK family proteins functions as a phosphor-peptide binding module. However, the GK domain of PSD-95 has been found to directly bind to a peptide sequence within the C-terminal region of neuronal-specific microtubule-associated protein 1A (MAP1A), although the detailed molecular mechanism governing this phosphorylation-independent interaction at the atomic level is missing. In the present study, we determine the crystal structure of PSD-95 GK in complex with the MAP1A peptide at 2.6-Å resolution. The complex structure reveals that, unlike a linear and elongated conformation in the phosphor-peptide/GK complexes, the MAP1A peptide adopts a unique conformation with a stretch of hydrophobic residues far from each other in the primary sequence clustering and interacting with the 'hydrophobic site' of PSD-95 GK and a highly conserved aspartic acid of MAP1A (D2117) mimicking the phosphor-serine/threonine in binding to the 'phosphor-site' of PSD-95 GK. We demonstrate that the MAP1A peptide may undergo a conformational transition upon binding to PSD-95 GK. Further structural comparison of known DLG GK-mediated complexes reveals the target recognition specificity and versatility of DLG GKs. © 2017 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society.

Entourage: Visualizing Relationships between Biological Pathways using Contextual Subsets

PubMed Central

Lex, Alexander; Partl, Christian; Kalkofen, Denis; Streit, Marc; Gratzl, Samuel; Wassermann, Anne Mai; Schmalstieg, Dieter; Pfister, Hanspeter

2014-01-01

Biological pathway maps are highly relevant tools for many tasks in molecular biology. They reduce the complexity of the overall biological network by partitioning it into smaller manageable parts. While this reduction of complexity is their biggest strength, it is, at the same time, their biggest weakness. By removing what is deemed not important for the primary function of the pathway, biologists lose the ability to follow and understand cross-talks between pathways. Considering these cross-talks is, however, critical in many analysis scenarios, such as judging effects of drugs. In this paper we introduce Entourage, a novel visualization technique that provides contextual information lost due to the artificial partitioning of the biological network, but at the same time limits the presented information to what is relevant to the analyst’s task. We use one pathway map as the focus of an analysis and allow a larger set of contextual pathways. For these context pathways we only show the contextual subsets, i.e., the parts of the graph that are relevant to a selection. Entourage suggests related pathways based on similarities and highlights parts of a pathway that are interesting in terms of mapped experimental data. We visualize interdependencies between pathways using stubs of visual links, which we found effective yet not obtrusive. By combining this approach with visualization of experimental data, we can provide domain experts with a highly valuable tool. We demonstrate the utility of Entourage with case studies conducted with a biochemist who researches the effects of drugs on pathways. We show that the technique is well suited to investigate interdependencies between pathways and to analyze, understand, and predict the effect that drugs have on different cell types. Fig. 1Entourage showing the Glioma pathway in detail and contextual information of multiple related pathways. PMID:24051820

Imaging Local Polarization in Ferroelectric Thin Films by Coherent X-Ray Bragg Projection Ptychography

NASA Astrophysics Data System (ADS)

Hruszkewycz, S. O.; Highland, M. J.; Holt, M. V.; Kim, Dongjin; Folkman, C. M.; Thompson, Carol; Tripathi, A.; Stephenson, G. B.; Hong, Seungbum; Fuoss, P. H.

2013-04-01

We used x-ray Bragg projection ptychography (BPP) to map spatial variations of ferroelectric polarization in thin film PbTiO3, which exhibited a striped nanoscale domain pattern on a high-miscut (001) SrTiO3 substrate. By converting the reconstructed BPP phase image to picometer-scale ionic displacements in the polar unit cell, a quantitative polarization map was made that was consistent with other characterization. The spatial resolution of 5.7 nm demonstrated here establishes BPP as an important tool for nanoscale ferroelectric domain imaging, especially in complex environments accessible with hard x rays.

Using freelisting to identify, assess, and characterize age differences in shared cultural domains.

PubMed

Schrauf, Robert W; Sanchez, Julia

2008-11-01

Freelisting is a brief, paper-and-pencil technique in which participants make lists of items that they believe belong in a particular domain. Where cultural domains are shared, as for young and old in the same society, subtle intracultural differences may be difficult to detect. This article presents a series of techniques for revealing and describing this intracultural variation in freelisted data among young versus old age groups. Older (N = 30) and younger (N = 31) Mexicans in Mexico City made freelists in four quotidian domains: animals, emotions, illnesses, and gendered occupations. We used minimum residual factor analysis (consensus analysis) to establish domain coherence and assess overall consensus concerning contents of the domains. We established subvariation within the overall consensus by comparing levels of observed versus predicted inter-informant agreement. Results showed divergent patterns of inter-informant agreement between young and old participants across domains. Qualitative examination of items with higher salience for young versus old revealed age differences consistent with prior findings in each domain. The concatenation of these techniques renders freelisting an accessible, easily administered tool for probing age and group differences in cultural domains.

Time Domain Stability Margin Assessment Method

NASA Technical Reports Server (NTRS)

Clements, Keith

2017-01-01

The baseline stability margins for NASA's Space Launch System (SLS) launch vehicle were generated via the classical approach of linearizing the system equations of motion and determining the gain and phase margins from the resulting frequency domain model. To improve the fidelity of the classical methods, the linear frequency domain approach can be extended by replacing static, memoryless nonlinearities with describing functions. This technique, however, does not address the time varying nature of the dynamics of a launch vehicle in flight. An alternative technique for the evaluation of the stability of the nonlinear launch vehicle dynamics along its trajectory is to incrementally adjust the gain and/or time delay in the time domain simulation until the system exhibits unstable behavior. This technique has the added benefit of providing a direct comparison between the time domain and frequency domain tools in support of simulation validation.

Time-Domain Stability Margin Assessment

NASA Technical Reports Server (NTRS)

Clements, Keith

2016-01-01

The baseline stability margins for NASA's Space Launch System (SLS) launch vehicle were generated via the classical approach of linearizing the system equations of motion and determining the gain and phase margins from the resulting frequency domain model. To improve the fidelity of the classical methods, the linear frequency domain approach can be extended by replacing static, memoryless nonlinearities with describing functions. This technique, however, does not address the time varying nature of the dynamics of a launch vehicle in flight. An alternative technique for the evaluation of the stability of the nonlinear launch vehicle dynamics along its trajectory is to incrementally adjust the gain and/or time delay in the time domain simulation until the system exhibits unstable behavior. This technique has the added benefit of providing a direct comparison between the time domain and frequency domain tools in support of simulation validation.

FREQUENCY MODULATION OF DIRECTLY IMAGED EXOPLANETS: GEOMETRIC EFFECT AS A PROBE OF PLANETARY OBLIQUITY

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kawahara, Hajime, E-mail: kawahara@eps.s.u-tokyo.ac.jp; Research Center for the Early Universe, School of Science, The University of Tokyo, Tokyo 113-0033

2016-05-10

We consider the time–frequency analysis of a scattered light curve of a directly imaged exoplanet. We show that the geometric effect due to planetary obliquity and orbital inclination induce the frequency modulation of the apparent diurnal periodicity. We construct a model of the frequency modulation and compare it with the instantaneous frequency extracted from the pseudo-Wigner distribution of simulated light curves of a cloudless Earth. The model provides good agreement with the simulated modulation factor, even for the light curve with Gaussian noise comparable to the signal. Notably, the shape of the instantaneous frequency is sensitive to the difference betweenmore » the prograde, retrograde, and pole-on spin rotations. While our technique requires the albedo map to be static, it does not need to solve the albedo map of the planet. The time–frequency analysis is complementary to other methods which utilize the amplitude modulation. This paper demonstrates the importance of the frequency domain of the photometric variability for the characterization of directly imaged exoplanets in future research.« less

Quantitative high-resolution mapping of phenanthrene sorption to black carbon particles.

PubMed

Obst, Martin; Grathwohl, Peter; Kappler, Andreas; Eibl, Oliver; Peranio, Nicola; Gocht, Tilman

2011-09-01

Sorption of hydrophobic organic contaminants such as polycyclic aromatic hydrocarbons (PAHs) to black carbon (BC) particles has been the focus of numerous studies. Conclusions on sorption mechanisms of PAH on BC were mostly derived from studies of sorption isotherms and sorption kinetics, which are based on batch experiments. However, mechanistic modeling approaches consider processes at the subparticle scale, some including transport within the pore-space or different spatial pore-domains. Direct evidence based on analytical techniques operating at the submicrometer scale for the location of sorption sites and the adsorbed species is lacking. In this work, we identified, quantified, and mapped the sorption of PAHs on different BC particles (activated carbon, charcoal and diesel soot) on a 25-100 nm scale using scanning transmission X-ray microscopy (STXM). In addition, we visualized the pore structure of the particles by transmission electron microscopy (TEM) on the 1-10 nm-scale. The combination of the chemical information from STXM with the physical information from TEM revealed that phenanthrene accumulates in the interconnected pore-system along primary "cracks" in the particles, confirming an adsorption mechanism.

A nearest-neighbor imputation approach to mapping tree species over large areas using forest inventory plots and moderate resolution raster data

Treesearch

B. Tyler Wilson; Andrew J. Lister; Rachel I. Riemann

2012-01-01

The paper describes an efficient approach for mapping multiple individual tree species over large spatial domains. The method integrates vegetation phenology derived from MODIS imagery and raster data describing relevant environmental parameters with extensive field plot data of tree species basal area to create maps of tree species abundance and distribution at a 250-...

In search of patient characteristics that may guide empirically based treatment selection for personality disorder patients-a concept map approach.

PubMed

van Manen, J G; Kamphuis, J H; Goossensen, A; Timman, R; Busschbach, J J V; Verheul, R

2012-08-01

Using the concept map method, this study aimed to summarize and describe patient characteristics pertinent to treatment selection for patients with personality disorders (PDs). Initial patient characteristics were derived from the research literature and a survey among Dutch expert clinicians. Concept mapping is a formalized conceptualization procedure that describes the underlying cognitive structures people use in complex tasks, such as treatment allocation. Based on expert opinions of 29 Dutch clinicians, a concept map was generated that yielded eight domains of patient characteristics, i.e., Severity of symptoms, Severity of personality pathology, Ego-adaptive capacities, Motivation and working alliance, Social context, Social demographic characteristics, Trauma, and Treatment history and medical condition. These domains can be ordered along two bipolar axes, running from internal to external concepts and from vulnerability to strength concepts, respectively. Our findings may serve as input for the delineation of algorithms for patient-treatment matching research in PD.

Laboratory multiple-crystal X-ray topography and reciprocal-space mapping of protein crystals: influence of impurities on crystal perfection

NASA Technical Reports Server (NTRS)

Hu, Z. W.; Thomas, B. R.; Chernov, A. A.

2001-01-01

Double-axis multiple-crystal X-ray topography, rocking-curve measurements and triple-axis reciprocal-space mapping have been combined to characterize protein crystals using a laboratory source. Crystals of lysozyme and lysozyme crystals doped with acetylated lysozyme impurities were examined. It was shown that the incorporation of acetylated lysozyme into crystals of lysozyme induces mosaic domains that are responsible for the broadening and/or splitting of rocking curves and diffraction-space maps along the direction normal to the reciprocal-lattice vector, while the overall elastic lattice strain of the impurity-doped crystals does not appear to be appreciable in high angular resolution reciprocal-space maps. Multiple-crystal monochromatic X-ray topography, which is highly sensitive to lattice distortions, was used to reveal the spatial distribution of mosaic domains in crystals which correlates with the diffraction features in reciprocal space. Discussions of the influence of acetylated lysozyme on crystal perfection are given in terms of our observations.

Laboratory multiple-crystal X-ray topography and reciprocal-space mapping of protein crystals: influence of impurities on crystal perfection.

PubMed

Hu, Z W; Thomas, B R; Chernov, A A

2001-06-01

Double-axis multiple-crystal X-ray topography, rocking-curve measurements and triple-axis reciprocal-space mapping have been combined to characterize protein crystals using a laboratory source. Crystals of lysozyme and lysozyme crystals doped with acetylated lysozyme impurities were examined. It was shown that the incorporation of acetylated lysozyme into crystals of lysozyme induces mosaic domains that are responsible for the broadening and/or splitting of rocking curves and diffraction-space maps along the direction normal to the reciprocal-lattice vector, while the overall elastic lattice strain of the impurity-doped crystals does not appear to be appreciable in high angular resolution reciprocal-space maps. Multiple-crystal monochromatic X-ray topography, which is highly sensitive to lattice distortions, was used to reveal the spatial distribution of mosaic domains in crystals which correlates with the diffraction features in reciprocal space. Discussions of the influence of acetylated lysozyme on crystal perfection are given in terms of our observations.

Image encryption with chaotic map and Arnold transform in the gyrator transform domains

NASA Astrophysics Data System (ADS)

Sang, Jun; Luo, Hongling; Zhao, Jun; Alam, Mohammad S.; Cai, Bin

2017-05-01

An image encryption method combing chaotic map and Arnold transform in the gyrator transform domains was proposed. Firstly, the original secret image is XOR-ed with a random binary sequence generated by a logistic map. Then, the gyrator transform is performed. Finally, the amplitude and phase of the gyrator transform are permutated by Arnold transform. The decryption procedure is the inverse operation of encryption. The secret keys used in the proposed method include the control parameter and the initial value of the logistic map, the rotation angle of the gyrator transform, and the transform number of the Arnold transform. Therefore, the key space is large, while the key data volume is small. The numerical simulation was conducted to demonstrate the effectiveness of the proposed method and the security analysis was performed in terms of the histogram of the encrypted image, the sensitiveness to the secret keys, decryption upon ciphertext loss, and resistance to the chosen-plaintext attack.

A Method of Surrogate Model Construction which Leverages Lower-Fidelity Information using Space Mapping Techniques

DTIC Science & Technology

2014-03-27

fidelity. This pairing is accomplished through the use of a space mapping technique, which is a process where the design space of a lower fidelity model...is aligned a higher fidelity model. The intent of applying space mapping techniques to the field of surrogate construction is to leverage the

Fitting the Jigsaw of Citation: Information Visualization in Domain Analysis.

ERIC Educational Resources Information Center

Chen, Chaomei; Paul, Ray J.; O'Keefe, Bob

2001-01-01

Discusses the role of information visualization in modeling and representing intellectual structures associated with scientific disciplines and visualizes the domain of computer graphics based on bibliographic data from author cocitation patterns. Highlights include author cocitation maps, citation time lines, animation of a high-dimensional…

Reconstructing the Surface Permittivity Distribution from Data Measured by the CONSERT Instrument aboard Rosetta: Method and Simulations

NASA Astrophysics Data System (ADS)

Plettemeier, D.; Statz, C.; Hegler, S.; Herique, A.; Kofman, W. W.

2014-12-01

One of the main scientific objectives of the Comet Nucleus Sounding Experiment by Radiowave Transmission (CONSERT) aboard Rosetta is to perform a dielectric characterization of comet 67P/Chuyurmov-Gerasimenko's nucleus by means of a bi-static sounding between the lander Philae launched onto the comet's surface and the orbiter Rosetta. For the sounding, the lander part of CONSERT will receive and process the radio signal emitted by the orbiter part of the instrument and transmit a signal to the orbiter to be received by CONSERT. CONSERT will also be operated as bi-static RADAR during the descent of the lander Philae onto the comet's surface. From data measured during the descent, we aim at reconstructing a surface permittivity map of the comet at the landing site and along the path below the descent trajectory. This surface permittivity map will give information on the bulk material right below and around the landing site and the surface roughness in areas covered by the instrument along the descent. The proposed method to estimate the surface permittivity distribution is based on a least-squares based inversion approach in frequency domain. The direct problem of simulating the wave-propagation between lander and orbiter at line-of-sight and the signal reflected on the comet's surface is modelled using a dielectric physical optics approximation. Restrictions on the measurement positions by the descent orbitography and limitations on the instrument dynamic range will be dealt with by application of a regularization technique where the surface permittivity distribution and the gradient with regard to the permittivity is projected in a domain defined by a viable model of the spatial material and roughness distribution. The least-squares optimization step of the reconstruction is performed in such domain on a reduced set of parameters yielding stable results. The viability of the proposed method is demonstrated by reconstruction results based on simulated data.

Pulling on the Long Tail with Flyover Country, a Mobile App to Expose, Visualize, Discover, and Explore Open Geoscience Data

NASA Astrophysics Data System (ADS)

Myrbo, A.; Loeffler, S.; Ai, S.; McEwan, R.

2015-12-01

The ultimate EarthCube product has been described as a mobile app that provides all of the known geoscience data for a geographic point or polygon, from the top of the atmosphere to the core of the Earth, throughout geologic time. The database queries are hidden from the user, and the data are visually rendered for easy recognition of patterns and associations. This fanciful vision is not so remote: NSF EarthCube and Geoinformatics support has already fostered major advances in database interoperability and harmonization of APIs; numerous "domain repositories," databases curated by subject matter experts, now provide a vast wealth of open, easily-accessible georeferenced data on rock and sediment chemistry and mineralogy, paleobiology, stratigraphy, rock magnetics, and more. New datasets accrue daily, including many harvested from the literature by automated means. None of these constitute big data - all are part of the long tail of geoscience, heterogeneous data consisting of relatively small numbers of measurements made by a large number of people, typically on physical samples. This vision of mobile data discovery requires a software package to cleverly expose these domain repositories' holdings; currently, queries mainly come from single investigators to single databases. The NSF-funded mobile app Flyover Country (FC; fc.umn.edu), developed for geoscience outreach and education, has been welcomed by data curators and cyberinfrastructure developers as a testing ground for their API services, data provision, and scalability. FC pulls maps and data within a bounding envelope and caches them for offline use; location-based services alert users to nearby points of interest (POI). The incorporation of data from multiple databases across domains requires parsimonious data requests and novel visualization techniques, especially for mapping of data with a time or stratigraphic depth component. The preservation of data provenance and authority is critical for researcher buy-in to all community databases, and further allows exploration and suggestions of collaborators, based upon geography and topical relevance.

Two techniques for mapping and area estimation of small grains in California using Landsat digital data

NASA Technical Reports Server (NTRS)

Sheffner, E. J.; Hlavka, C. A.; Bauer, E. M.

1984-01-01

Two techniques have been developed for the mapping and area estimation of small grains in California from Landsat digital data. The two techniques are Band Ratio Thresholding, a semi-automated version of a manual procedure, and LCLS, a layered classification technique which can be fully automated and is based on established clustering and classification technology. Preliminary evaluation results indicate that the two techniques have potential for providing map products which can be incorporated into existing inventory procedures and automated alternatives to traditional inventory techniques and those which currently employ Landsat imagery.

Capturing inhomogeneous broadening of the -CN stretch vibration in a Langmuir monolayer with high-resolution spectra and ultrafast vibrational dynamics in sum-frequency generation vibrational spectroscopy (SFG-VS)

NASA Astrophysics Data System (ADS)

Velarde, Luis; Wang, Hong-fei

2013-08-01

While in principle the frequency-domain and time-domain spectroscopic measurements should generate identical information for a given molecular system, the inhomogeneous character of surface vibrations in sum-frequency generation vibrational spectroscopy (SFG-VS) studies has only been studied with time-domain SFG-VS by mapping the decay of the vibrational polarization using ultrafast lasers, this due to the lack of SFG vibrational spectra with high enough spectral resolution and accurate enough lineshape. Here, with the recently developed high-resolution broadband SFG-VS (HR-BB-SFG-VS) technique, we show that the inhomogeneous lineshape can be obtained in the frequency-domain for the anchoring CN stretch of the 4-n-octyl-4'-cyanobiphenyl (8CB) Langmuir monolayer at the air-water interface, and that an excellent agreement with the time-domain SFG free-induction-decay can be established. We found that the 8CB CN stretch spectrum consists of a single peak centered at 2234.00 ± 0.01 cm-1 with a total linewidth of 10.9 ± 0.3 cm-1 at half maximum. The Lorentzian contribution accounts only for 4.7 ± 0.4 cm-1 to this width and the Gaussian (inhomogeneous) broadening for as much as 8.1 ± 0.2 cm-1. Polarization analysis of the -CN spectra showed that the -CN group is tilted 57° ± 2° from the surface normal. The large heterogeneity in the -CN spectrum is tentatively attributed to the -CN group interactions with the interfacial water molecules penetrated/accommodated into the 8CB monolayer, a unique phenomenon for the nCB Langmuir monolayers reported previously.

Capturing inhomogeneous broadening of the -CN stretch vibration in a Langmuir monolayer with high-resolution spectra and ultrafast vibrational dynamics in sum-frequency generation vibrational spectroscopy (SFG-VS).

PubMed

Velarde, Luis; Wang, Hong-fei

2013-08-28

While in principle the frequency-domain and time-domain spectroscopic measurements should generate identical information for a given molecular system, the inhomogeneous character of surface vibrations in sum-frequency generation vibrational spectroscopy (SFG-VS) studies has only been studied with time-domain SFG-VS by mapping the decay of the vibrational polarization using ultrafast lasers, this due to the lack of SFG vibrational spectra with high enough spectral resolution and accurate enough lineshape. Here, with the recently developed high-resolution broadband SFG-VS (HR-BB-SFG-VS) technique, we show that the inhomogeneous lineshape can be obtained in the frequency-domain for the anchoring CN stretch of the 4-n-octyl-4'-cyanobiphenyl (8CB) Langmuir monolayer at the air-water interface, and that an excellent agreement with the time-domain SFG free-induction-decay can be established. We found that the 8CB CN stretch spectrum consists of a single peak centered at 2234.00 ± 0.01 cm(-1) with a total linewidth of 10.9 ± 0.3 cm(-1) at half maximum. The Lorentzian contribution accounts only for 4.7 ± 0.4 cm(-1) to this width and the Gaussian (inhomogeneous) broadening for as much as 8.1 ± 0.2 cm(-1). Polarization analysis of the -CN spectra showed that the -CN group is tilted 57° ± 2° from the surface normal. The large heterogeneity in the -CN spectrum is tentatively attributed to the -CN group interactions with the interfacial water molecules penetrated/accommodated into the 8CB monolayer, a unique phenomenon for the nCB Langmuir monolayers reported previously.

The Evolutionary History of Protein Domains Viewed by Species Phylogeny

PubMed Central

Yang, Song; Bourne, Philip E.

2009-01-01

Background Protein structural domains are evolutionary units whose relationships can be detected over long evolutionary distances. The evolutionary history of protein domains, including the origin of protein domains, the identification of domain loss, transfer, duplication and combination with other domains to form new proteins, and the formation of the entire protein domain repertoire, are of great interest. Methodology/Principal Findings A methodology is presented for providing a parsimonious domain history based on gain, loss, vertical and horizontal transfer derived from the complete genomic domain assignments of 1015 organisms across the tree of life. When mapped to species trees the evolutionary history of domains and domain combinations is revealed, and the general evolutionary trend of domain and combination is analyzed. Conclusions/Significance We show that this approach provides a powerful tool to study how new proteins and functions emerged and to study such processes as horizontal gene transfer among more distant species. PMID:20041107

Mapping the binding domain of the F18 fimbrial adhesin.

PubMed

Smeds, A; Pertovaara, M; Timonen, T; Pohjanvirta, T; Pelkonen, S; Palva, A

2003-04-01

F18 fimbrial Esherichia coli strains are associated with porcine postweaning diarrhea and pig edema disease. Recently, the FedF subunit was identified as the adhesin of the F18 fimbriae. In this study, adhesion domains of FedF were further studied by constructing deletions within the fedF gene and expressing FedF proteins with deletions either together with the other F18 fimbrial subunits or as fusion proteins tagged with maltose binding protein. The region essential for adhesion to porcine intestinal epithelial cells was mapped between amino acid residues 60 and 109 of FedF. To map the binding domain even more closely, all eight charged amino acid residues within this region were independently replaced by alanine. Three of these single point mutants expressing F18 fimbriae exhibited significantly diminished capabilities to adhere to porcine epithelial cells in vitro. In addition, a triple point mutation and a double point mutation completely abolished receptor adhesiveness. The result further confirmed that the region between amino acid residues 60 and 109 is essential for the binding of F18 fimbriae to their receptor. In addition, the adhesion capability of the binding domain was eliminated after treatment with iodoacetamide, suggesting the formation of a disulfide bridge between Cys-63 and Cys-83, whereas Cys-111 and Cys-116 could be deleted without affecting the binding ability of FedF.

An Exploratory Study of Cost Engineering in Axiomatic Design: Creation of the Cost Model Based on an FR-DP Map

NASA Technical Reports Server (NTRS)

Lee, Taesik; Jeziorek, Peter

2004-01-01

Large complex projects cost large sums of money throughout their life cycle for a variety of reasons and causes. For such large programs, the credible estimation of the project cost, a quick assessment of the cost of making changes, and the management of the project budget with effective cost reduction determine the viability of the project. Cost engineering that deals with these issues requires a rigorous method and systematic processes. This paper introduces a logical framework to a&e effective cost engineering. The framework is built upon Axiomatic Design process. The structure in the Axiomatic Design process provides a good foundation to closely tie engineering design and cost information together. The cost framework presented in this paper is a systematic link between the functional domain (FRs), physical domain (DPs), cost domain (CUs), and a task/process-based model. The FR-DP map relates a system s functional requirements to design solutions across all levels and branches of the decomposition hierarchy. DPs are mapped into CUs, which provides a means to estimate the cost of design solutions - DPs - from the cost of the physical entities in the system - CUs. The task/process model describes the iterative process ot-developing each of the CUs, and is used to estimate the cost of CUs. By linking the four domains, this framework provides a superior traceability from requirements to cost information.

Advantage of spatial map ion imaging in the study of large molecule photodissociation

NASA Astrophysics Data System (ADS)

Lee, Chin; Lin, Yen-Cheng; Lee, Shih-Huang; Lee, Yin-Yu; Tseng, Chien-Ming; Lee, Yuan-Tseh; Ni, Chi-Kung

2017-07-01

The original ion imaging technique has low velocity resolution, and currently, photodissociation is mostly investigated using velocity map ion imaging. However, separating signals from the background (resulting from undissociated excited parent molecules) is difficult when velocity map ion imaging is used for the photodissociation of large molecules (number of atoms ≥ 10). In this study, we used the photodissociation of phenol at the S1 band origin as an example to demonstrate how our multimass ion imaging technique, based on modified spatial map ion imaging, can overcome this difficulty. The photofragment translational energy distribution obtained when multimass ion imaging was used differed considerably from that obtained when velocity map ion imaging and Rydberg atom tagging were used. We used conventional translational spectroscopy as a second method to further confirm the experimental results, and we conclude that data should be interpreted carefully when velocity map ion imaging or Rydberg atom tagging is used in the photodissociation of large molecules. Finally, we propose a modified velocity map ion imaging technique without the disadvantages of the current velocity map ion imaging technique.

A Geomorphological Approach To Landslide Susceptibility Assessment and Its Application To The Virginio River Basin

NASA Astrophysics Data System (ADS)

Casagli, N.; Catani, F.; Delmonaco, G.; Ermini, L.; Margottini, C.; Puglisi, C.

The present note presents the results of a research project aimed at developing a ge- omorphology based method for the assessment of landslide susceptibility. The work has been carried out in the Virginio River basin, a tributary of the Arno river with confluence located 20 km downstream from Florence (Italy). Starting from a detailed landslide inventory, essentially carried out by aerial-photograph survey, the first phase of the research was directed to geomorphic field investigations, aimed at determining those hillslope factors influencing landslide triggering. This analysis was carried out for a significant sub-sample of the inventoried landslides, allowing the distinction of the most relevant hillslope factors affecting each type of mass movement. Selected factors are a) the past slope gradient in which landslide originated, b) litology and 3) land use. Once defined as thematic vector data, these factors have been handled by GIS overlay mapping, allowing to single out, for the entire Virginio River basin, homogeneous domains (Unique Condition Units) that contain, for each landslide ty- pology, unique combinations of the selected hillslope factors. Those domains are the basic Terrain Units for the following phase of landslide susceptibility assessment and mapping. The hillslope factors not selected in the first phase, however playing an im- portant role in contributing to the activation of the mass movements, have been taken into account for the definition of a landslide susceptibility function. This function is es- sentially a logic function based on the presence/absence of preparatory factors within the previous selected Unique Condition Terrain Units. The final mapping of the ar- eas characterized by different landslide susceptibility levels was performed by vector and raster based GIS techniques on the basis of the number and rank of predisposing factors. These landslide susceptibility classes, defined by a logic and easily replicable function, can be useful in the decision making procedures connected with territorial planning.

Interactive roles of Ras, insulin receptor substrate-1, and proteins with Src homology-2 domains in insulin signaling in Xenopus oocytes.

PubMed

Chuang, L M; Hausdorff, S F; Myers, M G; White, M F; Birnbaum, M J; Kahn, C R

1994-11-04

Insulin receptor substrate-1 (IRS-1) serves as the major immediate substrate of insulin/insulin-like growth factor (IGF)-1 receptors and following tyrosine phosphorylation binds to specific Src homology-2 (SH2) domain-containing proteins including the p85 subunit of phosphatidylinositol (PI) 3-kinase and GRB2, a molecule believed to link IRS-1 to the Ras pathway. To investigate how these SH2-containing signaling molecules interact to regulate insulin/IGF-1 action, IRS-1, glutathione S-transferase (GST)-SH2 domain fusion proteins and Ras proteins were microinjected into Xenopus oocytes. We found that pleiotropic insulin actions are mediated by IRS-1 through two independent, but convergent, pathways involving PI 3-kinase and GRB2. Thus, microinjection of GST-fusion proteins of either p85 or GRB2 inhibited IRS-1-dependent activation of mitogen-activated protein (MAP) and S6 kinases and oocyte maturation, although only the GST-SH2 of p85 reduced insulin-stimulated PI 3-kinase activation. Co-injection of a dominant negative Ras (S17N) with IRS-1 inhibited insulin-stimulated MAP and S6 kinase activation. Micro-injection of activated [Arg12,Thr59]Ras increased basal MAP and S6 kinase activities and sensitized the oocytes to insulin-stimulated maturation without altering insulin-stimulated PI 3-kinase. The Ras-enhanced oocyte maturation response, but not the elevated basal level of MAP and S6 kinase, was partially blocked by the SH2-p85, but not SH2-GRB2. These data strongly suggest that IRS-1 can mediate many of insulin's actions on cellular enzyme activation and cell cycle progression requires binding and activation of multiple different SH2-domain proteins.

PSM/SH2-B distributes selected mitogenic receptor signals to distinct components in the PI3-kinase and MAP kinase signaling pathways.

PubMed

Deng, Youping; Xu, Hu; Riedel, Heimo

2007-02-15

The Pro-rich, PH, and SH2 domain containing mitogenic signaling adapter PSM/SH2-B has been implicated as a cellular partner of various mitogenic receptor tyrosine kinases and related signaling mechanisms. Here, we report in a direct comparison of three peptide hormones, that PSM participates in the assembly of distinct mitogenic signaling complexes in response to insulin or IGF-I when compared to PDGF in cultured normal fibroblasts. The complex formed in response to insulin or IGF-I involves the respective peptide hormone receptor and presumably the established components leading to MAP kinase activation. However, our data suggest an alternative link from the PDGF receptor via PSM directly to MEK1/2 and consequently also to p44/42 activation, possibly through a scaffold protein. At least two PSM domains participate, the SH2 domain anticipated to link PSM to the respective receptor and the Pro-rich region in an association with an unidentified downstream component resulting in direct MEK1/2 and p44/42 regulation. The PDGF receptor signaling complex formed in response to PDGF involves PI 3-kinase in addition to the same components and interactions as described for insulin or IGF-I. PSM associates with PI 3-kinase via p85 and in addition the PSM PH domain participates in the regulation of PI 3-kinase activity, presumably through membrane interaction. In contrast, the PSM Pro-rich region appears to participate only in the MAP kinase signal. Both pathways contribute to the mitogenic response as shown by cell proliferation, survival, and focus formation. PSM regulates p38 MAP kinase activity in a pathway unrelated to the mitogenic response.

Quantifying Patterns of Smooth Muscle Motility in the Gut and Other Organs With New Techniques of Video Spatiotemporal Mapping

PubMed Central

Lentle, Roger G.; Hulls, Corrin M.

2018-01-01

The uses and limitations of the various techniques of video spatiotemporal mapping based on change in diameter (D-type ST maps), change in longitudinal strain rate (L-type ST maps), change in area strain rate (A-type ST maps), and change in luminous intensity of reflected light (I-maps) are described, along with their use in quantifying motility of the wall of hollow structures of smooth muscle such as the gut. Hence ST-methods for determining the size, speed of propagation and frequency of contraction in the wall of gut compartments of differing geometric configurations are discussed. We also discuss the shortcomings and problems that are inherent in the various methods and the use of techniques to avoid or minimize them. This discussion includes, the inability of D-type ST maps to indicate the site of a contraction that does not reduce the diameter of a gut segment, the manipulation of axis [the line of interest (LOI)] of L-maps to determine the true axis of propagation of a contraction, problems with anterior curvature of gut segments and the use of adjunct image analysis techniques that enhance particular features of the maps. PMID:29686624

Mapping Joint Action.

ERIC Educational Resources Information Center

Slawski, Carl

The flow diagrams in this document provide cognitive maps to aid in synthesizing diverse areas of knowledge in a special brand of field theory. A model is presented which highlights the domains of structural functionalism (with concepts of cultural, personal and societal systems) and symbolic interactionism (with the concepts of self, sentiments…

Digital Mapping Techniques '08—Workshop Proceedings, Moscow, Idaho, May 18–21, 2008

USGS Publications Warehouse

Soller, David R.

2009-01-01

The Digital Mapping Techniques '08 (DMT'08) workshop was attended by more than 100 technical experts from 40 agencies, universities, and private companies, including representatives from 24 State geological surveys. This year's meeting, the twelfth in the annual series, was hosted by the Idaho Geological Survey, from May 18-21, 2008, on the University of Idaho campus in Moscow, Idaho. Each DMT workshop has been coordinated by the U.S. Geological Survey's National Geologic Map Database Project and the Association of American State Geologists (AASG). As in previous years' meetings, the objective was to foster informal discussion and exchange of technical information, principally in order to develop more efficient methods for digital mapping, cartography, GIS analysis, and information management. At this meeting, oral and poster presentations and special discussion sessions emphasized (1) methods for creating and publishing map products (here, "publishing" includes Web-based release); (2) field data capture software and techniques, including the use of LiDAR; (3) digital cartographic techniques; (4) migration of digital maps into ArcGIS Geodatabase format; (5) analytical GIS techniques; and (6) continued development of the National Geologic Map Database.

Comparing the Effects of Representational Tools in Collaborative and Individual Inquiry Learning

ERIC Educational Resources Information Center

Kolloffel, Bas; Eysink, Tessa H. S.; de Jong, Ton

2011-01-01

Constructing a representation in which students express their domain understanding can help them improve their knowledge. Many different representational formats can be used to express one's domain understanding (e.g., concept maps, textual summaries, mathematical equations). The format can direct students' attention to specific aspects of the…

Mapping University Students' Epistemic Framing of Computational Physics Using Network Analysis

ERIC Educational Resources Information Center

Bodin, Madelen

2012-01-01

Solving physics problem in university physics education using a computational approach requires knowledge and skills in several domains, for example, physics, mathematics, programming, and modeling. These competences are in turn related to students' beliefs about the domains as well as about learning. These knowledge and beliefs components are…

Time Domain Stability Margin Assessment of the NASA Space Launch System GN&C Design for Exploration Mission One

NASA Technical Reports Server (NTRS)

Clements, Keith; Wall, John

2017-01-01

The baseline stability margins for NASA's Space Launch System (SLS) launch vehicle were generated via the classical approach of linearizing the system equations of motion and determining the gain and phase margins from the resulting frequency domain model. To improve the fidelity of the classical methods, the linear frequency domain approach can be extended by replacing static, memoryless nonlinearities with describing functions. This technique, however, does not address the time varying nature of the dynamics of a launch vehicle in flight. An alternative technique for the evaluation of the stability of the nonlinear launch vehicle dynamics along its trajectory is to incrementally adjust the gain and/or time delay in the time domain simulation until the system exhibits unstable behavior. This technique has the added benefit of providing a direct comparison between the time domain and frequency domain tools in support of simulation validation.

Time Domain Stability Margin Assessment of the NS Space Launch System GN&C Design for Exploration Mission One

NASA Technical Reports Server (NTRS)

Clements, Keith; Wall, John

2017-01-01

The baseline stability margins for NASA's Space Launch System (SLS) launch vehicle were generated via the classical approach of linearizing the system equations of motion and determining the gain and phase margins from the resulting frequency domain model. To improve the fidelity of the classical methods, the linear frequency domain approach can be extended by replacing static, memoryless nonlinearities with describing functions. This technique, however, does not address the time varying nature of the dynamics of a launch vehicle in flight. An alternative technique for the evaluation of the stability of the nonlinear launch vehicle dynamics along its trajectory is to incrementally adjust the gain and/or time delay in the time domain simulation until the system exhibits unstable behavior. This technique has the added benefit of providing a direct comparison between the time domain and frequency domain tools in support of simulation validation.

Sequence stratigraphy, structural style, and age of deformation of the Malaita accretionary prism (Solomon arc-Ontong Java Plateau convergent zone)

NASA Astrophysics Data System (ADS)

Phinney, Eric J.; Mann, Paul; Coffin, Millard F.; Shipley, Thomas H.

2004-10-01

Possibilities for the fate of oceanic plateaus at subduction zones range from complete subduction of the plateau beneath the arc to complete plateau-arc accretion and resulting collisional orogenesis. Deep penetration, multi-channel seismic reflection (MCS) data from the northern flank of the Solomon Islands reveal the sequence stratigraphy, structural style, and age of deformation of an accretionary prism formed during late Neogene (5-0 Ma) convergence between the ˜33-km-thick crust of the Ontong Java oceanic plateau and the ˜15-km-thick Solomon island arc. Correlation of MCS data with the satellite-derived, free-air gravity field defines the tectonic boundaries and internal structure of the 800-km-long, 140-km-wide accretionary prism. We name this prism the "Malaita accretionary prism" or "MAP" after Malaita, the largest and best-studied island exposure of the accretionary prism in the Solomon Islands. MCS data, gravity data, and stratigraphic correlations to islands and ODP sites on the Ontong Java Plateau (OJP) reveal that the offshore MAP is composed of folded and thrust faulted sedimentary rocks and upper crystalline crust offscraped from the Solomon the subducting Ontong Java Plateau (Pacific plate) and transferred to the Solomon arc. With the exception of an upper, sequence of Quaternary? island-derived terrigenous sediments, the deformed stratigraphy of the MAP is identical to that of the incoming Ontong Java Plateau in the North Solomon trench. We divide the MAP into four distinct, folded and thrust fault-bounded structural domains interpreted to have formed by diachronous, southeast-to-northwest, and highly oblique entry of the Ontong Java Plateau into a former trench now marked by the Kia-Kaipito-Korigole (KKK) left-lateral strike-slip fault zone along the suture between the Solomon arc and the MAP. The structural style within each of the four structural domains consists of a parallel series of three to four fault propagation folds formed by the seaward propagation of thrust faults roughly parallel to sub-horizontal layering in the upper crystalline part of the OJP. Thrust fault offsets, spacing between thrusts, and the amplitude of related fault propagation folds progressively decrease to the west in the youngest zone of active MAP accretion (Choiseul structural domain). Surficial faulting and folding in the most recently deformed, northwestern domain show active accretion of greater than 1 km of sedimentary rock and 6 km, or about 20%, of the upper crystalline part of the OJP. The eastern MAP (Malaita and Ulawa domains) underwent an earlier, similar style of partial plateau accretion. A pre-late Pliocene age of accretion (˜3.4 Ma) is constrained by an onshore and offshore major angular unconformity separating Pliocene reefal limestone and conglomerate from folded and faulted pelagic limestone of Cretaceous to Miocene age. The lower 80% of the Ontong Java Plateau crust beneath the MAP thrust decollement appears unfaulted and unfolded and is continuous with a southwestward-dipping subducted slab of presumably denser plateau material beneath most of the MAP, and is traceable to depths >200 km in the mantle beneath the Solomon Islands.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lin, Jiusheng; van den Bedem, Henry; Brunger, Axel T.

Calmodulin (CaM) is the primary calcium signaling protein in eukaryotes and has been extensively studied using various biophysical techniques. Prior crystal structures have noted the presence of ambiguous electron density in both hydrophobic binding pockets of Ca 2+-CaM, but no assignment of these features has been made. In addition, Ca 2+-CaM samples many conformational substates in the crystal and accurately modeling the full range of this functionally important disorder is challenging. In order to characterize these features in a minimally biased manner, a 1.0 Å resolution single-wavelength anomalous diffraction data set was measured for selenomethionine-substituted Ca 2+-CaM. Density-modified electron-density mapsmore » enabled the accurate assignment of Ca 2+-CaM main-chain and side-chain disorder. These experimental maps also substantiate complex disorder models that were automatically built using low-contour features of model-phased electron density. Furthermore, experimental electron-density maps reveal that 2-methyl-2,4-pentanediol (MPD) is present in the C-terminal domain, mediates a lattice contact between N-terminal domains and may occupy the N-terminal binding pocket. The majority of the crystal structures of target-free Ca 2+-CaM have been derived from crystals grown using MPD as a precipitant, and thus MPD is likely to be bound in functionally critical regions of Ca 2+-CaM in most of these structures. The adventitious binding of MPD helps to explain differences between the Ca 2+-CaM crystal and solution structures and is likely to favor more open conformations of the EF-hands in the crystal.« less

Assessing potential climate change pressures across the conterminous United States: mapping plant hardiness zones, heat zones, growing degree days, and cumulative drought severity throughout this century

Treesearch

Stephen N. Matthews; Louis R. Iverson; Matthew P. Peters; Anantha M. Prasad

2018-01-01

The maps and tables presented here represent potential variability of projected climate change across the conterminous United States during three 30-year periods in this century and emphasizes the importance of evaluating multiple signals of change across large spatial domains. Maps of growing degree days, plant hardiness zones, heat zones, and cumulative drought...

Mapped Landmark Algorithm for Precision Landing

NASA Technical Reports Server (NTRS)

Johnson, Andrew; Ansar, Adnan; Matthies, Larry

2007-01-01

A report discusses a computer vision algorithm for position estimation to enable precision landing during planetary descent. The Descent Image Motion Estimation System for the Mars Exploration Rovers has been used as a starting point for creating code for precision, terrain-relative navigation during planetary landing. The algorithm is designed to be general because it handles images taken at different scales and resolutions relative to the map, and can produce mapped landmark matches for any planetary terrain of sufficient texture. These matches provide a measurement of horizontal position relative to a known landing site specified on the surface map. Multiple mapped landmarks generated per image allow for automatic detection and elimination of bad matches. Attitude and position can be generated from each image; this image-based attitude measurement can be used by the onboard navigation filter to improve the attitude estimate, which will improve the position estimates. The algorithm uses normalized correlation of grayscale images, producing precise, sub-pixel images. The algorithm has been broken into two sub-algorithms: (1) FFT Map Matching (see figure), which matches a single large template by correlation in the frequency domain, and (2) Mapped Landmark Refinement, which matches many small templates by correlation in the spatial domain. Each relies on feature selection, the homography transform, and 3D image correlation. The algorithm is implemented in C++ and is rated at Technology Readiness Level (TRL) 4.

Near-simultaneous hemoglobin saturation and oxygen tension maps in mouse brain using an AOTF microscope.

PubMed

Shonat, R D; Wachman, E S; Niu, W; Koretsky, A P; Farkas, D L

1997-09-01

A newly developed microscope using acousto-optic tunable filters (AOTFs) was used to generate in vivo hemoglobin saturation (SO2) and oxygen tension (PO2) maps in the cerebral cortex of mice. SO2 maps were generated from the spectral analysis of reflected absorbance images collected at different wavelengths, and PO2 maps were generated from the phosphorescence lifetimes of an injected palladium-porphyrin compound using a frequency-domain measurement. As the inspiratory O2 was stepped from hypoxia (10% O2), through normoxia (21% O2), to hyperoxia (60% O2), measured SO2 and PO2 levels rose accordingly and predictably throughout. A plot of SO2 versus PO2 in different arterial and venous regions of the pial vessels conformed to the sigmoidal shape of the oxygen-hemoglobin dissociation curve, providing further validation of the two mapping procedures. The study demonstrates the versatility of the AOTF microscope for in vivo physiologic investigation, allowing for the generation of nearly simultaneous SO2 and PO2 maps in the cerebral cortex, and the frequency-domain detection of phosphorescence lifetimes. This class of study opens up exciting new possibilities for investigating the dynamics of hemoglobin and O2 binding during functional activation of neuronal tissues.

Near-simultaneous hemoglobin saturation and oxygen tension maps in mouse brain using an AOTF microscope.

PubMed Central

Shonat, R D; Wachman, E S; Niu, W; Koretsky, A P; Farkas, D L

1997-01-01

A newly developed microscope using acousto-optic tunable filters (AOTFs) was used to generate in vivo hemoglobin saturation (SO2) and oxygen tension (PO2) maps in the cerebral cortex of mice. SO2 maps were generated from the spectral analysis of reflected absorbance images collected at different wavelengths, and PO2 maps were generated from the phosphorescence lifetimes of an injected palladium-porphyrin compound using a frequency-domain measurement. As the inspiratory O2 was stepped from hypoxia (10% O2), through normoxia (21% O2), to hyperoxia (60% O2), measured SO2 and PO2 levels rose accordingly and predictably throughout. A plot of SO2 versus PO2 in different arterial and venous regions of the pial vessels conformed to the sigmoidal shape of the oxygen-hemoglobin dissociation curve, providing further validation of the two mapping procedures. The study demonstrates the versatility of the AOTF microscope for in vivo physiologic investigation, allowing for the generation of nearly simultaneous SO2 and PO2 maps in the cerebral cortex, and the frequency-domain detection of phosphorescence lifetimes. This class of study opens up exciting new possibilities for investigating the dynamics of hemoglobin and O2 binding during functional activation of neuronal tissues. Images FIGURE 1 FIGURE 3 FIGURE 4 FIGURE 6 PMID:9284290

Optical detection of gold nanoparticles in a prostate-shaped porcine phantom.

PubMed

Grabtchak, Serge; Tonkopi, Elena; Whelan, William M

2013-07-01

Gold nanoparticles can be used as molecular contrast agents binding specifically to cancer sites and thus delineating tumor regions. Imaging gold nanoparticles deeply embedded in tissues with optical techniques possesses significant challenges due to multiple scattering of optical photons that blur the obtained images. Both diagnostic and therapeutic applications can benefit from a minimally invasive technique that can identify, localize, and quantify the payloads of gold nanoparticles deeply embedded in biological tissues. An optical radiance technique is applied to map localized inclusions of gold nanorods in 650- to 900-nm spectral range in a porcine phantom that mimics prostate geometry. Optical radiance defines a variation in the angular density of photons impinging on a selected point in the tissue from various directions. The inclusions are formed by immersing a capillary filled with gold nanorods in the phantom at increasing distances from the detecting fiber. The technique allows the isolation of the spectroscopic signatures of the inclusions from the background and identification of inclusion locations in the angular domain. Detection of ∼4×1010 gold nanoparticles or 0.04  mg Au/mL (detector-inclusion separation 10 mm, source-detector separation 15 mm) in the porcine tissue is demonstrated. The encouraging results indicate a promising potential of radiance spectroscopy in early prostate cancer diagnostics with gold nanoparticles.

What Google Maps can do for biomedical data dissemination: examples and a design study.

PubMed

Jianu, Radu; Laidlaw, David H

2013-05-04

Biologists often need to assess whether unfamiliar datasets warrant the time investment required for more detailed exploration. Basing such assessments on brief descriptions provided by data publishers is unwieldy for large datasets that contain insights dependent on specific scientific questions. Alternatively, using complex software systems for a preliminary analysis may be deemed as too time consuming in itself, especially for unfamiliar data types and formats. This may lead to wasted analysis time and discarding of potentially useful data. We present an exploration of design opportunities that the Google Maps interface offers to biomedical data visualization. In particular, we focus on synergies between visualization techniques and Google Maps that facilitate the development of biological visualizations which have both low-overhead and sufficient expressivity to support the exploration of data at multiple scales. The methods we explore rely on displaying pre-rendered visualizations of biological data in browsers, with sparse yet powerful interactions, by using the Google Maps API. We structure our discussion around five visualizations: a gene co-regulation visualization, a heatmap viewer, a genome browser, a protein interaction network, and a planar visualization of white matter in the brain. Feedback from collaborative work with domain experts suggests that our Google Maps visualizations offer multiple, scale-dependent perspectives and can be particularly helpful for unfamiliar datasets due to their accessibility. We also find that users, particularly those less experienced with computer use, are attracted by the familiarity of the Google Maps API. Our five implementations introduce design elements that can benefit visualization developers. We describe a low-overhead approach that lets biologists access readily analyzed views of unfamiliar scientific datasets. We rely on pre-computed visualizations prepared by data experts, accompanied by sparse and intuitive interactions, and distributed via the familiar Google Maps framework. Our contributions are an evaluation demonstrating the validity and opportunities of this approach, a set of design guidelines benefiting those wanting to create such visualizations, and five concrete example visualizations.

What google maps can do for biomedical data dissemination: examples and a design study

PubMed Central

2013-01-01

Background Biologists often need to assess whether unfamiliar datasets warrant the time investment required for more detailed exploration. Basing such assessments on brief descriptions provided by data publishers is unwieldy for large datasets that contain insights dependent on specific scientific questions. Alternatively, using complex software systems for a preliminary analysis may be deemed as too time consuming in itself, especially for unfamiliar data types and formats. This may lead to wasted analysis time and discarding of potentially useful data. Results We present an exploration of design opportunities that the Google Maps interface offers to biomedical data visualization. In particular, we focus on synergies between visualization techniques and Google Maps that facilitate the development of biological visualizations which have both low-overhead and sufficient expressivity to support the exploration of data at multiple scales. The methods we explore rely on displaying pre-rendered visualizations of biological data in browsers, with sparse yet powerful interactions, by using the Google Maps API. We structure our discussion around five visualizations: a gene co-regulation visualization, a heatmap viewer, a genome browser, a protein interaction network, and a planar visualization of white matter in the brain. Feedback from collaborative work with domain experts suggests that our Google Maps visualizations offer multiple, scale-dependent perspectives and can be particularly helpful for unfamiliar datasets due to their accessibility. We also find that users, particularly those less experienced with computer use, are attracted by the familiarity of the Google Maps API. Our five implementations introduce design elements that can benefit visualization developers. Conclusions We describe a low-overhead approach that lets biologists access readily analyzed views of unfamiliar scientific datasets. We rely on pre-computed visualizations prepared by data experts, accompanied by sparse and intuitive interactions, and distributed via the familiar Google Maps framework. Our contributions are an evaluation demonstrating the validity and opportunities of this approach, a set of design guidelines benefiting those wanting to create such visualizations, and five concrete example visualizations. PMID:23642009

The Development of Combined Raman Spectroscopy-Optical Coherence Tomography and Application for Skin Cancer Diagnosis

NASA Astrophysics Data System (ADS)

Patil, Chetan

2009-11-01

Optical spectroscopy and imaging have shown promise for performing rapid, non-invasive disease detection and diagnosis in vivo. Independently, Raman Spectroscopy (RS) has demonstrated the ability to perform diagnosis of epithelial cancers such the cervix with excellent overall classification accuracy due to the inherent biochemical specificity of the technique, however relating features of tissue morphology with techniques such as Raman mapping is clinically impractical due to the weak nature of the scattering phenomena resulting in prohibitively long acquisition times. Optical Coherence Tomography (OCT), on the other hand, has demonstrated the ability to perform real-time, high-resolution, cross-sectional imaging of the microstructural characteristics of disease, but typically lacks molecularly specific information that can assist in classifying pathological lesions. We present the development of a combined Raman Spectroscopy-OCT (RS-OCT) instrument capable of compensating for the limitations of each technique individually and performing both biochemical and microstructural evaluation of tissues. We will include the design and development of benchtop RS-OCT implementations based on independent 785 nm Raman and 1310 nm time-domain OCT system backbones, as well as with a 785nm Raman / 850nm spectral-domain OCT setup employing an integrated detection arm. These systems motivated the ultimate design of a clinical RS-OCT system for application in dermatology. In order to aid in the development of our Raman spectral processing and classification methods, we conducted a simultaneous pilot study in which RS alone was used to measure basal and squamous cell carcinomas. We will present the initial results from our clinical experiences with the combined RS-OCT device, and include a discussion of spectral classification and the ultimate potential of combined RS-OCT for skin cancer diagnosis.

Ontology Mappings to Improve Learning Resource Search

ERIC Educational Resources Information Center

Gasevic, Dragan; Hatala, Marek

2006-01-01

This paper proposes an ontology mapping-based framework that allows searching for learning resources using multiple ontologies. The present applications of ontologies in e-learning use various ontologies (eg, domain, curriculum, context), but they do not give a solution on how to interoperate e-learning systems based on different ontologies. The…

Translation of Bernstein Coefficients Under an Affine Mapping of the Unit Interval

NASA Technical Reports Server (NTRS)

Alford, John A., II

2012-01-01

We derive an expression connecting the coefficients of a polynomial expanded in the Bernstein basis to the coefficients of an equivalent expansion of the polynomial under an affine mapping of the domain. The expression may be useful in the calculation of bounds for multi-variate polynomials.

Metrics and Mappings: A Framework for Understanding Real-World Quantitative Estimation.

ERIC Educational Resources Information Center

Brown, Norman R.; Siegler, Robert S.

1993-01-01

A metrics and mapping framework is proposed to account for how heuristics, domain-specific reasoning, and intuitive statistical induction processes are integrated to generate estimates. Results of 4 experiments involving 188 undergraduates illustrate framework usefulness and suggest when people use heuristics and when they emphasize…

PREVENTING CONTAMINATION OF PUBLIC WATER SUPPLY WELLS USING COMPUTERIZED MODELING AND MAPPING TOOLS

EPA Science Inventory

The EPA Office of Research and Development and the Office of Ground Water and Drinking Water have collaborated since 1998 on the development of a public domain ground-water flow modeling system designed to facilitate capture zone delineation and protection area mapping for public...

Finding Mutual Exclusion Invariants in Temporal Planning Domains

NASA Technical Reports Server (NTRS)

Bernardini, Sara; Smith, David E.

2011-01-01

We present a technique for automatically extracting temporal mutual exclusion invariants from PDDL2.2 planning instances. We first identify a set of invariant candidates by inspecting the domain and then check these candidates against properties that assure invariance. If these properties are violated, we show that it is sometimes possible to refine a candidate by adding additional propositions and turn it into a real invariant. Our technique builds on other approaches to invariant synthesis presented in the literature, but departs from their limited focus on instantaneous discrete actions by addressing temporal and numeric domains. To deal with time, we formulate invariance conditions that account for both the entire structure of the operators (including the conditions, rather than just the effects) and the possible interactions between operators. As a result, we construct a technique that is not only capable of identifying invariants for temporal domains, but is also able to find a broader set of invariants for non-temporal domains than the previous techniques.

Application of the Yoshida-Ruth Techniques to Implicit Integration and Multi-Map Explicit Integration

DOE Office of Scientific and Technical Information (OSTI.GOV)

Forest, E.; Bengtsson, J.; Reusch, M.F.

1991-04-01

The full power of Yoshida's technique is exploited to produce an arbitrary order implicit symplectic integrator and multi-map explicit integrator. This implicit integrator uses a characteristic function involving the force term alone. Also we point out the usefulness of the plain Ruth algorithm in computing Taylor series map using the techniques first introduced by Berz in his 'COSY-INFINITY' code.

Optimization of spatial frequency domain imaging technique for estimating optical properties of food and biological materials

USDA-ARS?s Scientific Manuscript database

Spatial frequency domain imaging technique has recently been developed for determination of the optical properties of food and biological materials. However, accurate estimation of the optical property parameters by the technique is challenging due to measurement errors associated with signal acquis...

Birefringence measurement of retinal nerve fiber layer using polarization-sensitive spectral domain optical coherence tomography with Jones matrix based analysis

NASA Astrophysics Data System (ADS)

Yamanari, Masahiro; Miura, Masahiro; Makita, Shuichi; Yatagai, Toyohiko; Yasuno, Yoshiaki

2007-02-01

Birefringence of retinal nerve fiber layer is measured by polarization-sensitive spectral domain optical coherence tomography using the B-scan-oriented polarization modulation method. Birefringence of the optical fiber and the cornea is compensated by Jones matrix based analysis. Three-dimensional phase retardation map around the optic nerve head and en-face phase retardation map of the retinal nerve fiber layer are shown. Unlike scanning laser polarimetry, our system can measure the phase retardation quantitatively without using bow-tie pattern of the birefringence in the macular region, which enables diagnosis of glaucoma even if the patients have macular disease.

An Ontology-Enabled Natural Language Processing Pipeline for Provenance Metadata Extraction from Biomedical Text (Short Paper).

PubMed

Valdez, Joshua; Rueschman, Michael; Kim, Matthew; Redline, Susan; Sahoo, Satya S

2016-10-01

Extraction of structured information from biomedical literature is a complex and challenging problem due to the complexity of biomedical domain and lack of appropriate natural language processing (NLP) techniques. High quality domain ontologies model both data and metadata information at a fine level of granularity, which can be effectively used to accurately extract structured information from biomedical text. Extraction of provenance metadata, which describes the history or source of information, from published articles is an important task to support scientific reproducibility. Reproducibility of results reported by previous research studies is a foundational component of scientific advancement. This is highlighted by the recent initiative by the US National Institutes of Health called "Principles of Rigor and Reproducibility". In this paper, we describe an effective approach to extract provenance metadata from published biomedical research literature using an ontology-enabled NLP platform as part of the Provenance for Clinical and Healthcare Research (ProvCaRe). The ProvCaRe-NLP tool extends the clinical Text Analysis and Knowledge Extraction System (cTAKES) platform using both provenance and biomedical domain ontologies. We demonstrate the effectiveness of ProvCaRe-NLP tool using a corpus of 20 peer-reviewed publications. The results of our evaluation demonstrate that the ProvCaRe-NLP tool has significantly higher recall in extracting provenance metadata as compared to existing NLP pipelines such as MetaMap.

The Development of a Conceptual Framework and Preliminary Item Bank for Childbirth-Specific Patient-Reported Outcome Measures.

PubMed

Korst, Lisa M; Fridman, Moshe; Saeb, Samia; Greene, Naomi; Fink, Arlene; Gregory, Kimberly D

2018-05-24

To develop a conceptual framework and preliminary item bank for childbirth-specific patient-reported outcome (PRO) domains. Women, who were U.S. residents, ≥18 years old, and ≥20 weeks pregnant, were surveyed regarding their childbirth values and preferences (V&P) using online panels. Using community-based research techniques and Patient-Reported Outcomes Management Information System (PROMIS ® ) methodology, we conducted a comprehensive literature review to identify self-reported survey items regarding patient-reported V&P and childbirth experiences and outcomes (PROs). The V&P/PRO domains were validated by focus groups. We conducted a cross-sectional observational study and fitted a multivariable logistic regression model to each V&P item to describe "who" wanted each item. We identified 5,880 V&P/PRO items that mapped to 19 domains and 58 subdomains. We present results for the 2,250 survey respondents who anticipated a vaginal delivery in a hospital. Wide variation existed regarding each V&P item, and personal characteristics, such as maternal confidence and ability to cope well with pain, were frequent predictors in the models. The resulting preliminary item bank consisted of 60 key personal characteristics and 63 V&P/PROs. The conceptual framework and preliminary (PROMIS ® ) item bank presented here provide a foundation for the development of childbirth-specific V&P/PROs. © Health Research and Educational Trust.

Structural Insights into Triglyceride Storage Mediated by Fat Storage-Inducing Transmembrane (FIT) Protein 2

PubMed Central

Gross, David A.; Snapp, Erik L.; Silver, David L.

2010-01-01

Fat storage-Inducing Transmembrane proteins 1 & 2 (FIT1/FITM1 and FIT2/FITM2) belong to a unique family of evolutionarily conserved proteins localized to the endoplasmic reticulum that are involved in triglyceride lipid droplet formation. FIT proteins have been shown to mediate the partitioning of cellular triglyceride into lipid droplets, but not triglyceride biosynthesis. FIT proteins do not share primary sequence homology with known proteins and no structural information is available to inform on the mechanism by which FIT proteins function. Here, we present the experimentally-solved topological models for FIT1 and FIT2 using N-glycosylation site mapping and indirect immunofluorescence techniques. These methods indicate that both proteins have six-transmembrane-domains with both N- and C-termini localized to the cytosol. Utilizing this model for structure-function analysis, we identified and characterized a gain-of-function mutant of FIT2 (FLL(157-9)AAA) in transmembrane domain 4 that markedly augmented the total number and mean size of lipid droplets. Using limited-trypsin proteolysis we determined that the FLL(157-9)AAA mutant has enhanced trypsin cleavage at K86 relative to wild-type FIT2, indicating a conformational change. Taken together, these studies indicate that FIT2 is a 6 transmembrane domain-containing protein whose conformation likely regulates its activity in mediating lipid droplet formation. PMID:20520733

High Fidelity Raman Chemical Imaging of Materials

NASA Astrophysics Data System (ADS)

Bobba, Venkata Nagamalli Koteswara Rao

The development of high fidelity Raman imaging systems is important for a number of application areas including material science, bio-imaging, bioscience and healthcare, pharmaceutical analysis, and semiconductor characterization. The use of Raman imaging as a characterization tool for detecting the amorphous and crystalline regions in the biopolymer poly-L-lactic acid (PLLA) is the precis of my thesis. In the first chapter, a brief insight about the basics of Raman spectroscopy, Raman chemical imaging, Raman mapping, and Raman imaging techniques has been provided. The second chapter contains details about the successful development of tailored sample of PLLA. Biodegradable polymers are used in areas of tissue engineering, agriculture, packaging, and in medical field for drug delivery, implant devices, and surgical sutures. Detailed information about the sample preparation and characterization of these cold-drawn PLLA polymer substrates has been provided. Wide-field Raman hyperspectral imaging using an acousto-optic tunable filter (AOTF) was demonstrated in the early 1990s. The AOTF contributed challenges such as image walk, distortion, and image blur. A wide-field AOTF Raman imaging system has been developed as part of my research and methods to overcome some of the challenges in performing AOTF wide-field Raman imaging are discussed in the third chapter. This imaging system has been used for studying the crystalline and amorphous regions on the cold-drawn sample of PLLA. Of all the different modalities that are available for performing Raman imaging, Raman point-mapping is the most extensively used method. The ease of obtaining the Raman hyperspectral cube dataset with a high spectral and spatial resolution is the main motive of performing this technique. As a part of my research, I have constructed a Raman point-mapping system and used it for obtaining Raman hyperspectral image data of various minerals, pharmaceuticals, and polymers. Chapter four offers information about the techniques used for characterization of pharmaceutical drugs and mapping of the crystalline domains in polymers. In addition, image processing algorithms that yield chemical-based image contrast have been designed to better enable quantitative estimates of chemical heterogeneity. Some of the problems that are needed to be solved for image processing and the need for developing a volumetric imaging system is discussed in chapter five.

Extensible Ontological Modeling Framefork for Subject Mediation

NASA Astrophysics Data System (ADS)

Kalinichenko, L. A.; Skvortsov, N. A.

An approach for extensible ontological model construction in a mediation environment intended for heterogeneous information sources integration in various subject domains is presented. A mediator ontological language (MOL) may depend on a subject domain and is to be defined at the mediator consolidation phase. On the other hand, for different information sources different ontological models (languages) can be used to define their own ontologies. Reversible mapping of the source ontological models into MOL is needed for information sources registration at the mediator. An approach for such reversible mapping is demonstrated for a class of the Web information sources. It is assumed that such sources apply the DAML+OIL ontological model. A subset of the hybrid object-oriented and semi-structured canonical mediator data model is used for the core of MOL. Construction of a reversible mapping of DAML+OIL into an extension of the core of MOL is presented in the paper. Such mapping is a necessary pre-requisite for contextualizing and registration of information sources at the mediator. The mapping shows how extensible MOL can be constructed. The approach proposed is oriented on digital libraries where retrieval is focused on information content, rather than on information entities.

Correlation mapping microscopy

NASA Astrophysics Data System (ADS)

McGrath, James; Alexandrov, Sergey; Owens, Peter; Subhash, Hrebesh M.; Leahy, Martin J.

2015-03-01

Changes in the microcirculation are associated with conditions such as Raynauds disease. Current modalities used to assess the microcirculation such as nailfold capillaroscopy are limited due to their depth ambiguity. A correlation mapping technique was recently developed to extend the capabilities of Optical Coherence Tomography to generate depth resolved images of the microcirculation. Here we present the extension of this technique to microscopy modalities, including confocal microscopy. It is shown that this correlation mapping microscopy technique can extend the capabilities of conventional microscopy to enable mapping of vascular networks in vivo with high spatial resolution.

Time-resolved multicolor two-photon excitation fluorescence microscopy of cells and tissues

NASA Astrophysics Data System (ADS)

Zheng, Wei

2014-11-01

Multilabeling which maps the distribution of different targets is an indispensable technique in many biochemical and biophysical studies. Two-photon excitation fluorescence (TPEF) microscopy of endogenous fluorophores combining with conventional fluorescence labeling techniques such as genetically encoded fluorescent protein (FP) and fluorescent dyes staining could be a powerful tool for imaging living cells. However, the challenge is that the excitation and emission wavelength of these endogenous fluorophores and fluorescent labels are very different. A multi-color ultrafast source is required for the excitation of multiple fluorescence molecules. In this study, we developed a two-photon imaging system with excitations from the pump femtosecond laser and the selected supercontinuum generated from a photonic crystal fiber (PCF). Multiple endogenous fluorophores, fluorescent proteins and fluorescent dyes were excited in their optimal wavelengths simultaneously. A time- and spectral-resolved detection system was used to record the TPEF signals. This detection technique separated the TPEF signals from multiple sources in time and wavelength domains. Cellular organelles such as nucleus, mitochondria, microtubule and endoplasmic reticulum, were clearly revealed in the TPEF images. The simultaneous imaging of multiple fluorophores of cells will greatly aid the study of sub-cellular compartments and protein localization.

A Deformable Smart Skin for Continuous Sensing Based on Electrical Impedance Tomography.

PubMed

Visentin, Francesco; Fiorini, Paolo; Suzuki, Kenji

2016-11-16

In this paper, we present a low-cost, adaptable, and flexible pressure sensor that can be applied as a smart skin over both stiff and deformable media. The sensor can be easily adapted for use in applications related to the fields of robotics, rehabilitation, or costumer electronic devices. In order to remove most of the stiff components that block the flexibility of the sensor, we based the sensing capability on the use of a tomographic technique known as Electrical Impedance Tomography. The technique allows the internal structure of the domain under study to be inferred by reconstructing its conductivity map. By applying the technique to a material that changes its resistivity according to applied forces, it is possible to identify these changes and then localise the area where the force was applied. We tested the system when applied to flat and curved surfaces. For all configurations, we evaluate the artificial skin capabilities to detect forces applied over a single point, over multiple points, and changes in the underlying geometry. The results are all promising, and open the way for the application of such sensors in different robotic contexts where deformability is the key point.